madhavsuresh / chimerascan Goto Github PK
View Code? Open in Web Editor NEWAutomatically exported from code.google.com/p/chimerascan
License: GNU General Public License v3.0
Automatically exported from code.google.com/p/chimerascan
License: GNU General Public License v3.0
Test chimera detection performance with BWA as the initial alignment tool
Original issue reported on code.google.com by [email protected]
on 2 Aug 2011 at 3:01
What steps will reproduce the problem?
1. Running on one of my pairs of fastq files always seems to crash in the same
place
2.
3.
What is the expected output? What do you see instead?
I assume it is crashing, but I dont know why. Other samples succeeded using
the same configuration. There is no more information other than the output ends
with:
2013-10-01 12:16:09,037 - root - INFO - Extracting single-mapped reads that may
span breakpoints
2013-10-01 12:16:09,039 - root - DEBUG - Matching single-mapped frags to 5'
chimeras
What version of the product are you using? On what operating system?
chimerascan-0.4.3-1
on Gnu Linux
Please provide any additional information below.
Contents of my tmp directory
3.7G Sep 27 19:28 reads_2.fq
3.7G Sep 27 19:29 reads_1.fq
602M Sep 27 21:07 unaligned_1.fq
602M Sep 27 21:07 unaligned_2.fq
143K Sep 27 21:07 maxmulti_1.fq
143K Sep 27 21:07 maxmulti_2.fq
1.3G Sep 28 00:09 realigned_reads.bam
749M Sep 28 03:52 gene_paired_reads.bam
522M Sep 28 03:52 genome_paired_reads.bam
262M Sep 28 03:52 unmapped_reads.bam
885K Sep 28 03:52 complex_reads.bam
92M Sep 28 03:55 discordant_reads.bedpe
92M Sep 28 03:56 discordant_reads.srt.bedpe
5.4G Sep 28 05:18 encompassing_chimeras.txt
1.9G Sep 28 05:34 encompassing_chimeras.filtered.txt
1.9G Sep 28 05:41 encompassing_chimeras.breakpoint_sorted.txt
58M Sep 28 05:47 breakpoints.fa
61M Sep 28 05:48 breakpoints.txt
14M Sep 28 05:48 breakpoints.4.ebwt
2.5M Sep 28 05:48 breakpoints.3.ebwt
27M Sep 28 05:49 breakpoints.1.ebwt
6.8M Sep 28 05:49 breakpoints.2.ebwt
27M Sep 28 05:52 breakpoints.rev.1.ebwt
6.8M Sep 28 05:52 breakpoints.rev.2.ebwt
718K Sep 28 05:56 encomp_spanning_reads.fq
58M Sep 28 06:01 unaligned_spanning_reads.fq
410M Sep 28 06:08 singlemap_reads.srt.bam
4.3M Sep 28 06:08 singlemap_reads.srt.bam.bai
0 Oct 1 14:42 tmp_singlemap_seqs.txt
Original issue reported on code.google.com by [email protected]
on 1 Oct 2013 at 7:00
What steps will reproduce the problem?
1. #CHIMERASCAN-0.4.5 setup
export
PYTHONPATH=/shared/app/chimerascan-0.4.5/lib64/python2.6/site-packages:$PYTHONPA
TH
export PATH=/shared/app/chimerascan-0.4.5/chimerascan/:$PATH
python /shared/app/chimerascan-0.4.5/chimerascan/chimerascan_run.py -p 8
/shared/app/BOWTIE/indexes/CHIMERASCAN_INDEXES $a1 $a2
/home/hazards/Project_DW/Sample_99/Nov14_CHIMERASCAN_OUT
2. $a1 $a2 are variables referring to specific read pair fastq files
3. I am running the program on human lung derived RNASeq fastq generated by an
Illumina sequencer
What is the expected output? What do you see instead?
chimeras.bedpe was expected
Here's what I see:
.
.
.
2013-11-15 09:18:55,808 - root - WARNING - Could not extract sequence of length
>101 from 3' partner at gene_uc002ect.2:0-101, only retrieved sequence of
length 94
2013-11-15 09:18:56,438 - root - WARNING - Could not extract sequence of length
>101 from 3' partner at gene_uc010vft.1:0-101, only retrieved sequence of
length 90
2013-11-15 09:18:56,771 - root - WARNING - Could not extract sequence of length
>101 from 5' partner at gene_uc011mtj.1:0-96, only retrieved sequence of length
96
2013-11-15 09:19:06,915 - root - WARNING - Could not extract sequence of length
>101 from 3' partner at gene_uc010zpm.1:1741-1842, only retrieved sequence of
length 99
2013-11-15 09:19:09,269 - root - INFO - Filtering encompassing chimeras with
few supporting reads
2013-11-15 09:57:34,874 - root - INFO - Extracting breakpoint sequences from
chimeras
2013-11-15 10:16:30,598 - root - INFO - Building bowtie index of breakpoint
spanning sequences
2013-11-15 10:35:32,445 - root - INFO - Extracting encompassing reads that may
extend past breakpoints
2013-11-15 10:51:26,686 - root - INFO - Separating unmapped and single-mapping
reads that may span breakpoints
2013-11-15 11:05:38,719 - root - INFO - Extracting single-mapped reads that may
span breakpoints
/home/hazards/.lsbatch/1384447987.22825.shell: line 42: 10199 Killed
python /shared/app/chimerascan-0.4.5/chimerascan/chimerascan_run.py -p 8
/shared/app/BOWTIE/indexes/CHIMERASCAN_INDEXES
What version of the product are you using? On what operating system?
Chimerscan 0.4.5
Bowtie 1.0.0
Python 2.6.6
RHEL 6.2 Linux
LSF 7.2
Please provide any additional information below.
The log files suggest that the initial runs complete through
isize_dist.txt, breakpoint_bowtie_index.log, and tmp_singlemap_seqs.txt
-rw-r--r-- 1 hazards hazards 1446 Nov 15 07:23 runconfig.xml
-rw-r--r-- 1 hazards hazards 5449339058 Nov 15 09:33 aligned_reads.bam
-rw-r--r-- 1 hazards hazards 7386269125 Nov 15 10:45 sorted_aligned_reads.bam
-rw-r--r-- 1 hazards hazards 9578704 Nov 15 10:48
sorted_aligned_reads.bam.bai
-rw-r--r-- 1 hazards hazards 6613 Nov 15 10:48 isize_dist.txt
drwxr-xr-x 2 hazards hazards 104 Nov 16 20:22 log
drwxr-xr-x 2 hazards hazards 8192 Nov 16 21:38 tmp
Sample_86/Nov14_CHIMERASCAN_OUT/log:
total 24
-rw-r--r-- 1 hazards hazards 465 Nov 15 09:33 bowtie_alignment.log
-rw-r--r-- 1 hazards hazards 457 Nov 15 15:07 bowtie_trimmed_realignment.log
-rw-r--r-- 1 hazards hazards 12663 Nov 16 20:53 breakpoint_bowtie_index.log
Sample_86/Nov14_CHIMERASCAN_OUT/tmp:
total 110869964
-rw-r--r-- 1 hazards hazards 5797564944 Nov 15 08:03 reads_2.fq
-rw-r--r-- 1 hazards hazards 5797564944 Nov 15 08:03 reads_1.fq
-rw-r--r-- 1 hazards hazards 1792743679 Nov 15 09:32 unaligned_1.fq
-rw-r--r-- 1 hazards hazards 1792743679 Nov 15 09:32 unaligned_2.fq
-rw-r--r-- 1 hazards hazards 193024 Nov 15 09:32 maxmulti_1.fq
-rw-r--r-- 1 hazards hazards 193024 Nov 15 09:32 maxmulti_2.fq
-rw-r--r-- 1 hazards hazards 4876081081 Nov 15 15:07 realigned_reads.bam
-rw-r--r-- 1 hazards hazards 3120178382 Nov 15 23:38 gene_paired_reads.bam
-rw-r--r-- 1 hazards hazards 2072258813 Nov 15 23:38 genome_paired_reads.bam
-rw-r--r-- 1 hazards hazards 635025773 Nov 15 23:38 unmapped_reads.bam
-rw-r--r-- 1 hazards hazards 934624 Nov 15 23:38 complex_reads.bam
-rw-r--r-- 1 hazards hazards 295327399 Nov 15 23:45 discordant_reads.bedpe
-rw-r--r-- 1 hazards hazards 295327399 Nov 15 23:45 discordant_reads.srt.bedpe
-rw-r--r-- 1 hazards hazards 49046649769 Nov 16 17:34 encompassing_chimeras.txt
-rw-r--r-- 1 hazards hazards 17552465613 Nov 16 19:26
encompassing_chimeras.filtered.txt
-rw-r--r-- 1 hazards hazards 17552465613 Nov 16 19:47
encompassing_chimeras.breakpoint_sorted.txt
-rw-r--r-- 1 hazards hazards 603862877 Nov 16 20:22 breakpoints.fa
-rw-r--r-- 1 hazards hazards 652818329 Nov 16 20:22 breakpoints.txt
-rw-r--r-- 1 hazards hazards 140401371 Nov 16 20:23 breakpoints.4.ebwt
-rw-r--r-- 1 hazards hazards 25023302 Nov 16 20:23 breakpoints.3.ebwt
-rw-r--r-- 1 hazards hazards 234699054 Nov 16 20:39 breakpoints.1.ebwt
-rw-r--r-- 1 hazards hazards 70200692 Nov 16 20:39 breakpoints.2.ebwt
-rw-r--r-- 1 hazards hazards 234699054 Nov 16 20:53 breakpoints.rev.1.ebwt
-rw-r--r-- 1 hazards hazards 70200692 Nov 16 20:53 breakpoints.rev.2.ebwt
-rw-r--r-- 1 hazards hazards 3878595 Nov 16 21:27 encomp_spanning_reads.fq
-rw-r--r-- 1 hazards hazards 212324326 Nov 16 21:32
unaligned_spanning_reads.fq
-rw-r--r-- 1 hazards hazards 649644709 Nov 16 21:38 singlemap_reads.srt.bam
-rw-r--r-- 1 hazards hazards 5238976 Nov 16 21:38
singlemap_reads.srt.bam.bai
-rw-r--r-- 1 hazards hazards 0 Nov 16 21:38 tmp_singlemap_seqs.txt
I run the program on a local research cluster whose nodes have either 16Mb ram
or 24Gb ram. restricting to the 24Gb ram machines has no effect. ie the program
still runs and gets killed. I would assume that there is a size limitation but
the some files as large as 5-7 Gb have completed while others fail as
described. Re-running the jobs that fail repeats the failure.
Original issue reported on code.google.com by [email protected]
on 18 Nov 2013 at 9:59
Provide a BAM file in the final output containing the chimeric reads.
Will enable visualization of reads in genome browsers
Original issue reported on code.google.com by [email protected]
on 2 Dec 2011 at 5:24
What steps will reproduce the problem?
Running chimerascan-0.4.5 with command line arguments with Paired End RNA-Seq
data
What is the expected output? What do you see instead?
A <filename>.bedpe was expected output.
I see the error "'bowtie-build' failed to create breakpoint index" instead.
What version of the product are you using? On what operating system?
chimerascan-0.4.5, OS is Linux compute000 2.6.32-220.el6.x86_64 #1 SMP Wed Nov
9 08:03:13 EST 2011 x86_64 x86_64 x86_64 GNU/Linux
Please provide any additional information below.
I am not sure why it failed, because I ran it previously for other sample and
chimerascan ran for 3-4 days but did give me a result .bedpe file.
Original issue reported on code.google.com by [email protected]
on 9 Apr 2014 at 3:22
Develop fast scripts to interconvert between transcriptomic and genomic
coordinates.
This will facilitate building a purely genomic BAM file with mapping results
for viewing using genome browsers
Original issue reported on code.google.com by [email protected]
on 2 Dec 2011 at 5:29
What steps will reproduce the problem?
2014-03-11 22:31:04,573 - root - INFO - Sorting BEDPE file
Traceback (most recent call last):
File "/usr/local/bin/chimerascan_run.py", line 1002, in <module>
main()
File "/usr/local/bin/chimerascan_run.py", line 999, in main
sys.exit(run_chimerascan(runconfig))
File "/usr/local/bin/chimerascan_run.py", line 659, in run_chimerascan
tmp_dir=tmp_dir)
File "/usr/local/lib64/python2.6/site-packages/chimerascan/pipeline/discordant_reads_to_bedpe.py", line 92, in sort_bedpe
tempdirs=tempdirs)
File "/usr/local/lib64/python2.6/site-packages/chimerascan/lib/batch_sort.py", line 46, in batch_sort
output_chunk = open(os.path.join(tempdir,'%06i'%len(chunks)),'w+b',64*1024)
IOError: [Errno 24] Too many open files:
'/home/calogero/Documents/data/fusion_comparison/positive.tests/MCF-7/illu/1st/t
mp/001020'
It seems that the there is a limits in the number of files that Python can open.
What is the expected output? What do you see instead?
No output the program stops because of the above error
What version of the product are you using? On what operating system?
chimerascan-0.4.5 on Suse Enterprise
Please provide any additional information below.
I attached the nohup.out file of the run.
I also add the commands used to run chimerascan
nohup chimerascan_run.py /home/calogero/bin/chimerascan-0.4.5/index -v -p 64
--filter-unique-frags=2 --library-type=fr-firststrand
/home/calogero/Documents/data/fusion_comparison/positive.tests/MCF-7/illu/MCF7w4
e8spikesmrna_S1_L001_R1_001.fastq
/home/calogero/Documents/data/fusion_comparison/positive.tests/MCF-7/illu/MCF7w4
e8spikesmrna_S1_L002_R1_001.fastq
/home/calogero/Documents/data/fusion_comparison/positive.tests/MCF-7/illu/1st &
nohup chimerascan_run.py /home/calogero/bin/chimerascan-0.4.5/index -v -p 64
--filter-unique-frags=2 --library-type=fr-secondstrand
/home/calogero/Documents/data/fusion_comparison/positive.tests/MCF-7/illu/MCF7w4
e8spikesmrna_S1_L001_R1_001.fastq
/home/calogero/Documents/data/fusion_comparison/positive.tests/MCF-7/illu/MCF7w4
e8spikesmrna_S1_L002_R1_001.fastq
/home/calogero/Documents/data/fusion_comparison/positive.tests/MCF-7/illu/2nd &
Original issue reported on code.google.com by [email protected]
on 12 Mar 2014 at 6:46
Attachments:
The sequencing library I am dealing with requires trimming of 15 bases on the
reverse read only, so I end up with 100 base Fwd read and an 85 base Rev read.
When I run chimerascan with these files it gives me an error that the pairs are
different lengths. I decided maybe that was just a sanity check, so I commented
out the check for equal length pairs and re-ran it. It seems to run ok. Is
there any issue with this? Do reads have to be the same length?
I did notice that when looking for discordant reads there were some errors
saying something like:
2014-10-16 16:15:12,503 - root - WARNING - Could not extract sequence of length
>101 from 5' partner at gene_uc031ret.1:0-42, only retrieved sequence of length
42
but I am not sure this is related?
Original issue reported on code.google.com by [email protected]
on 20 Oct 2014 at 6:57
Use mismatch information (e.g. the MD tag in SAM) to trim read alignments that
have mismatches in the first/last bases. This splash occurs when aligning
chimeric reads that span a junction by <= 2 bases (or the number of allowed
mismatches in the alignment tool).
Trim the beginning/end of the joined reads to eliminate these leading/trailing
mismatches and improve alignment.
Current solution is to simple add/subtract 2 from read alignments during
chimera nomination phase.
Original issue reported on code.google.com by [email protected]
on 17 Jan 2011 at 6:55
Hello,
where I can found a detailed description of all files into the tmp folder?
Thanks,
Best regards
Francesca
Original issue reported on code.google.com by [email protected]
on 9 Jan 2014 at 9:51
What steps will reproduce the problem?
1. Run analysis using version "0.5.0" from the SVN repo; pysam version "0.7.5"
2. Use default settings and "-p 4" on a 16 core machine
What is the expected output? What do you see instead?
Expected: results, instead: an error message in realigned_reads.log:
Traceback (most recent call last):
File "/usr/local/lib/python2.7/dist-packages/chimerascan/pipeline/sam_to_bam_pesr.py", line 68, in <module>
sys.exit(main())
File "/usr/local/lib/python2.7/dist-packages/chimerascan/pipeline/sam_to_bam_pesr.py", line 65, in main
return sam_to_bam_pesr(args.input_sam_file, args.input_fastq_file, args.output_bam_file)
File "/usr/local/lib/python2.7/dist-packages/chimerascan/pipeline/sam_to_bam_pesr.py", line 34, in sam_to_bam_pesr
assert r.qname == fqrec.qname
AssertionError
Error while flushing and closing output
terminate called after throwing an instance of 'int'
What version of the product are you using? On what operating system?
* chimerascan "0.5.0" (from SVN repo)
* pysam "0.7.5" (from tar.gz source)
* Debian, saucy
Please provide any additional information below.
The tool was running for quite some time:
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
2013-11-04 15:53:41,981 - root - DEBUG - Reading transcript features
2013-11-04 15:53:42,861 - root - DEBUG - Creating genome SAM header
2013-11-04 15:53:45,063 - root - DEBUG - Creating transcript to genome map
2013-11-04 15:53:45,363 - root - DEBUG - Converting transcriptome to genome BAM
61460496 reads; of these:
61460496 (100.00%) were paired; of these:
21692002 (35.29%) aligned concordantly 0 times
20838036 (33.90%) aligned concordantly exactly 1 time
18930458 (30.80%) aligned concordantly >1 times
64.71% overall alignment rate
2013-11-04 22:07:04,670 - root - DEBUG - Paired fragments: 39768494
2013-11-04 22:07:04,748 - root - DEBUG - Unpaired fragments: 21692002
2013-11-04 22:07:04,758 - root - DEBUG - Found 122920992 fragments
I hope you can fix this issue; it occurs in all my samples.
Best regards,
Youri
Original issue reported on code.google.com by [email protected]
on 5 Nov 2013 at 8:47
We have observed certain sets of reads that have poor quality bases at the 3'
end. This can cause 3' end segments to be unmapped, and place a greater burden
on the segmented alignment phase. Not only is this slower, but it will
inevitably lead to a greater number of false positives (garbage in => garbage
out).
Dynamic read trimming is a viable solution here. The first goal is to follow
the BWA trimming paradigm.
Note that this feature cannot be enabled until variable length reads are fully
supported throughout the pipeline. There are still areas where fixed length
reads are assumed and shortcuts are taken.
Original issue reported on code.google.com by [email protected]
on 10 Feb 2011 at 4:20
Hello,
where can i get detailed explanation for header of chimerascan bedpe file. e.g. chimera classes based on orientation of genes
Thanks and Regards,
Pawan
Original issue reported on code.google.com by [email protected]
on 20 Aug 2013 at 2:41
What steps will reproduce the problem?
3.
What is the expected output? What do you see instead?
html file should be created. However, I got:
=======
/usr/local/bin/chimerascan_html_table.py: line 5:
Created on Feb 12, 2011
@author: mkiyer
: command not found
=======
What version of the product are you using? On what operating system?
v0.3.3. The OS is sles11 sp1
Please provide any additional information below.
standard test following the wiki page
Original issue reported on code.google.com by [email protected]
on 25 Feb 2011 at 6:04
Thanks to the deFuse project for this nice idea.
For each candidate chimera, compare the sequence of the candidate 3' partner
with the sequence of the normal gene. Count the number of bases of exact
homology at the junction and include this information when remapping to find
junction spanning reads.
When tallying the junction spanning reads, only count reads that span further
than the regions of homology in the 5'/3' partners.
Implementing this additional filter is trivial and should account for a lot of
the candidates with large numbers of junction-spanning reads with a small
amount of "anchor".
Not high priority because we have other means of filtering these reads.
Original issue reported on code.google.com by [email protected]
on 5 Feb 2011 at 4:57
Dear Chimerascan authors,
I have paired end reads with ~500 bp library size (as set by the wet-lab) with
104 per Illumina reads. with this design, I was wondering what the fragment
size will be for the discordant reads detection. Will that be 500bp? or
something else?
Also, should I specific the insert size or will the program automatically
estimate insert size based on initial alignments?
Also, is there any way you could include IGV screenshots
showing a successful chimera detected by the algorithm?
I am running chimerascan 0.4.3 on 64-bit linux
Thank you.
------------
Step 6: Discover discordant reads
The realigned reads are searched for evidence of discordant reads. A discordant
read is currently defined as follows:
1. The fragment does not align to the genome within user-specified fragment size range (default: 1000bp)
2. The pair does not align to a single transcript
3. The pair does not align to different transcripts that share exonic sequences on the same strand. In otherwords, reads that map to different isoforms of the same gene are excluded, as it is not the goal of chimerascan to discover unannotated splicing patterns within a single gene.
Original issue reported on code.google.com by [email protected]
on 12 Oct 2011 at 9:30
add an option to run chimerascan from gzipped fastq files
Original issue reported on code.google.com by [email protected]
on 17 Feb 2011 at 7:40
Hello,
I am getting an error message when running the indexer:
Traceback (most recent call last):
File "bin/chimerascan_index.py", line 32, in <module>
import chimerascan.pysam as pysam
File "/home/carmenise/chimerascan-0.4.5/chimerascan/pysam/__init__.py", line 1, in <module>
from csamtools import *
ImportError: No module named csamtools
What should I do to fix it ?
Thank you
Original issue reported on code.google.com by [email protected]
on 10 Jun 2013 at 1:06
Single reads mapped as multiple segments may reveal indels and small
rearrangements. These can be detected by finding reads with split mappings to
the same gene, but where the segment mappings are not contiguous.
It would be a relatively small task to add checks for these types of
aberrations and report them as a complementary module to fusion discovery
Original issue reported on code.google.com by [email protected]
on 18 Jan 2011 at 12:57
Hi, this is not really a issue. It is rather a new feature.
I am wondering if is possible to run the filtering (step 12) as a standalone
step. We would like to play with the filtering part of the parameters a bit but
it seems like a waste of computation if we just rerun the whole pipeline.
Thanks,
Yupu
Original issue reported on code.google.com by [email protected]
on 20 Sep 2012 at 6:55
Assume for segments 1,2,3,4. If segment 2 is unmapped due to multimapping the
joiner will output split reads for segment 1, segment 2, and segments 3-4. If
we check segment 2 for the multimapping (XM) tag in bowtie and allow the
segment joining logic to skip segments, we could potentially recover segment 2
(infer its position based on the positions of the other segments) and not need
to report a split.
Original issue reported on code.google.com by [email protected]
on 15 Jan 2011 at 8:21
There is a linker error on some system.
All that is required to fix it is adding the static keyword to the following
inlined function:
https://code.google.com/p/chimerascan/source/browse/tags/chimerascan_v0.4.3.1/ch
imerascan/pysam/samtools/ksort.h#144
Original issue reported on code.google.com by [email protected]
on 16 May 2014 at 10:50
What steps will reproduce the problem?
pgm=~/bin/Chimerascan/chimerascan-0.4.5/bin/chimerascan_index.py
genome=/users/rg/projects/references/Genome/H.sapiens/hg19/Homo_sapiens.GRCh37.c
hromosomes.chr.M.fa
module purge
module load Bowtie/0.12.7-goolf-1.4.10-no-OFED
time python $pgm $genome hg19.ucsc_genes.txt hg19_ucsc_genes_Index 2>
hg19_ucsc_genes_Index/chimerascan_index_ucscgenes.err >
hg19_ucsc_genes_Index/chimerascan_index_ucscgenes.out
What is the expected output? What do you see instead?
The chimerascan index. I do not see it, but those files:
ll hg19_ucsc_genes_Index/
total 4.6G
-rw-r--r-- 1 sdjebali CRG_Lab_Roderic_Guigo 17M Jan 9 15:44 gene_features.txt
-rw-r--r-- 1 sdjebali CRG_Lab_Roderic_Guigo 3.2G Jan 9 15:44 align_index.fa
-rw-r--r-- 1 sdjebali CRG_Lab_Roderic_Guigo 2.7M Jan 9 15:45 align_index.fa.fai
-rw-r--r-- 1 sdjebali CRG_Lab_Roderic_Guigo 730M Jan 9 15:46 align_index.4.ebwt
-rw-r--r-- 1 sdjebali CRG_Lab_Roderic_Guigo 651K Jan 9 15:46 align_index.3.ebwt
-rw-r--r-- 1 sdjebali CRG_Lab_Roderic_Guigo 0 Jan 9 15:46 align_index.2.ebwt
What version of the product are you using? On what operating system?
chimerascan-0.4.5 on Linux ant-login5.linux.crg.es 2.6.32-504.1.3.el6.x86_64 #1
SMP Tue Nov 11 14:19:04 CST 2014 x86_64 x86_64 x86_64 GNU/Linux
Please provide any additional information below.
I ran the chimerascan indexer with the ucsc gene file provided here, the hg19
genome without haplotypes and Bowtie 0.12.7, and I get the following error
message after several minutes:
[fai_load] build FASTA index.
2015-01-09 15:45:21,906 - root - INFO - Building bowtie index
2015-01-09 16:04:02,486 - root - ERROR - bowtie-build failed to create
alignment index
together with a core.
Any idea why?
Original issue reported on code.google.com by [email protected]
on 9 Jan 2015 at 5:03
Add support for variable read lengths. Most of this functionality is already
built-in, but need to develop unit-tests and try this.
Variable read length support will allow trimming based on read qualities in the
initial read parsing stage
Original issue reported on code.google.com by [email protected]
on 14 Jan 2011 at 6:40
Add A's to the end of each transcript in order to align poly-a tail reads and
improve sensitivity.
Original issue reported on code.google.com by [email protected]
on 4 Jul 2011 at 2:41
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.