rishavray/pilfer

piRNA cluster prediction and analysis framework

pilfer's Issues

Pilfer Job killed.

Hello,

I tried to get a piRNA cluster using your script pilfer.py. For a gzipped fastq file of size 573.0 Mb, I have got bam file from hg19 alignment using bowtie of size 2.9 Gb and bed file of size 9.2 Gb after subtracting it with ncRNA.bed. When I tried the following command
(python27) vivekr@sarabhai:~$ python /home/vivekr/PILFER/tools/pilfer.py -i /home/vivekr/piRNA/SRR7541164.bed > /home/vivekr/piRNA/SRR7541164.pirna_cluster

Killed

After very long pause, the job was killed. Does very heavy bed file responsible for this?

I cannot locate ncrna.bed, retro-transposons.bed anywhere in the zip file, i assume the script you have provided is according to your folders

Adapter trimming
Running Collapse
Reading from file ./trimmed/HI.3965.005.RPI1.1-1_R1.fastq.gz
Processing reads
Original number of reads: 16651798
collapsed number of reads: 732060
Mapping to hg19
piRNA alignment
Filtering SAM
[samopen] SAM header is present: 26719 sequences.
HI.3965.005.RPI1.1-1_R1
[samopen] SAM header is present: 26719 sequences.
[samopen] SAM header is present: 26719 sequences.
rm: cannot remove './hg19_sam/HI.3965.005.RPI1.1-1_R1.sam': No such file or directory
Making BED files
Error: Unable to open file /data/sata_data/home/tmhrnaseq/pirna/ncrna/ncrna.bed. Exiting.
Traceback (most recent call last):
File "./tools/pilfer.py", line 2, in
import numpy as np
ImportError: No module named numpy
python: can't open file 'union.py': [Errno 2] No such file or directory
Merging clusters
Traceback (most recent call last):
File "./tools/merge_cluster.py", line 16, in
next(csvin)
StopIteration
TE profiling
HI.3965.005.RPI1.1-1_R1
Error: Unable to open file /data/sata_data/home/tmhrnaseq/pirna/retro-transposons.bed. Exiting.
Traceback (most recent call last):
File "./tools/merge.py", line 7, in
row1 = csvin.next()
StopIteration
Traceback (most recent call last):
File "./tools/merge.py", line 7, in
row1 = csvin.next()
StopIteration
Traceback (most recent call last):
File "./tools/merge.py", line 7, in
row1 = csvin.next()
StopIteration
Traceback (most recent call last):
File "./tools/merge.py", line 7, in
row1 = csvin.next()
StopIteration

Question about multimapping reads

Hi,

I would like to try PILFER to predict piRNA clusters in three distinct species, but I have some questions about multi-mapping reads.

• Does PILFER work with multi-mapping reads? If so, how many alignments per read is the maximum allowed?
• It is possible to "reallocate" multimapping reads? With "reallocate" I mean weight each alignment of a multi-mapping read based on the density of reads in the surrounding region.
• In case the answer to the previous questions is "yes", does PILFER works only with Bowtie or it can work with other not standalone mappers, such as sRNAmapper.pl (the mapper used in the prediction with proTRAC).

Thank you very much.

Best regards,
Adrià.

The union step

Hi, I use the pipeline to do the analysis in Rat, I first use you sample to run. But met one problem in union.py step.
Could you help me check it? Thanks

bedtools subtract -b human-dataset/gencode28-human-ncRNA.bed -a sample_input.bed -s -f 0.5 -A > bed/cluster/sample_input
echo sample_input >> prefix_list
python tools/union.py prefix_list ./bed/cluster/ > cluster_union.tsv
awk 'NR>1{print $1}' cluster_union.tsv
chrY
chrX
chr13
chr12
chr11
chr10
chr17
chr16
chr15
chr14
chr19
chr18
chrM
chr22
chr20
chr21
chr7
chr6
chr5
chr4
chr3
chr2
chr1
chr9
chr8