pachterlab/bears_analyses

Examples of kallisto + sleuth

bears_analyses's Issues

Trapnell data

http://trace.ncbi.nlm.nih.gov/Traces/study/?acc=SRP012607

You only want a subset of the data (all the ones that contain hiseq) and perform differential expression against "transfection" (scramble versus hox1kd)

A nested parallel experiment demonstrates differences in intensity-dependence between RNA-seq and microarrays

https://nar.oxfordjournals.org/content/early/2015/06/30/nar.gkv636.full
SRA: PRJNA271248

Where to find/download SRA design matrix and config.json file information

Hello,

I am looking to find SRA design matrix and config.json file information for the 6 runs of Study SRP014759 on SRA website. The paper introducing the Lair, by Pimentel et al., says that design matrix can be found from the SRA, but I am not sure where to look.

Thanks.

Study of gene expression changes in TH-MYCN murine neuroblastomas in response to 24hr of panobinostat treatment

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE69869

Normalization of RNA-seq data using factor analysis of control genes or samples (Zebrafish)

http://www.nature.com/nbt/journal/v32/n9/full/nbt.2931.html
http://www.sciencedirect.com/science/article/pii/S0896627314000051
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53334

ABA Is Required for Plant Acclimation to a Combination of Salt and Heat Stress

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0147625

One more data set

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0017820#s5

http://www.ncbi.nlm.nih.gov/sra/?term=SRA026846.1

Two conditions for mouse RNA-Seq, one condition contains 10 samples and the other contains 11 samples.

In-Depth Duodenal Transcriptome Survey in Chickens with Divergent Feed Efficiency Using RNA-Seq

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0136765
http://www.ncbi.nlm.nih.gov/sra/SRP055561

A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages

http://www.nature.com/ncomms/2014/140210/ncomms4230/full/ncomms4230.html
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53960

Shared index style

A few things about the shared index:

• When looking at the urls in species.json, I don't seem to see the actual url of the file. Are you prefixing it somewhere with the ensembl the url? It would be best to simply have a generic url for this
• The kmer length should be included in the index file name. To be clear, you can have 1 fasta to many indices

That's all I can think of for now. Will look at it more closely later.

Nikaido missing reads?

I ran snakemake -p in the Nikaido directory on the most recent commit on the lucille2 server,
and got the output below. Have I done something wrong, or are the Nikaido reads missing?

wget -O annotation/Latimeria_chalumnae.LatCha1.rel79.cdna.all.fa.gz http://bio.math.berkeley.edu/kallisto/transcriptomes/Latimeria_chalumnae.LatCha1.rel79.cdna.all.fa.gz
--2016-03-23 10:08:08--  http://bio.math.berkeley.edu/kallisto/transcriptomes/Latimeria_chalumnae.LatCha1.rel79.cdna.all.fa.gz
Resolving bio.math.berkeley.edu (bio.math.berkeley.edu)... 128.32.213.142
Connecting to bio.math.berkeley.edu (bio.math.berkeley.edu)|128.32.213.142|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 16135641 (15M) [application/x-gzip]
Saving to: ‘annotation/Latimeria_chalumnae.LatCha1.rel79.cdna.all.fa.gz’

100%[===========================================================================================================================================>] 16,135,641  --.-K/s   in 0.1s    

2016-03-23 10:08:08 (104 MB/s) - ‘annotation/Latimeria_chalumnae.LatCha1.rel79.cdna.all.fa.gz’ saved [16135641/16135641]

1 of 41 steps (2%) done
rule kallisto_index:
        input: annotation/Latimeria_chalumnae.LatCha1.rel79.cdna.all.fa.gz
        output: annotation/Latimeria_chalumnae.LatCha1.rel79.cdna.all.kidx
kallisto index -k 21 -i annotation/Latimeria_chalumnae.LatCha1.rel79.cdna.all.kidx annotation/Latimeria_chalumnae.LatCha1.rel79.cdna.all.fa.gz

[build] loading fasta file annotation/Latimeria_chalumnae.LatCha1.rel79.cdna.all.fa.gz
[build] k-mer length: 21
[build] warning: clipped off poly-A tail (longer than 10)
        from 25 target sequences
[build] warning: replaced 85470 non-ACGUT characters in the input sequence
        with pseudorandom nucleotides
[build] counting k-mers ... done.           
[build] building target de Bruijn graph ... ^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B^[[B done 
[build] creating equivalence classes ...  done
[build] target de Bruijn graph has 422728 contigs and contains 44955722 k-mers 

2 of 41 steps (5%) done
rule fastq_dump_paired:
        output: data/paired/DRR002308, data/paired/DRR002308/DRR002308_1.fastq.gz, data/paired/DRR002308/DRR002308_2.fastq.gz
        benchmark: benchmarks/DRR002308/fastq_dump.json
fastq-dump --split-files -O data/paired/DRR002308 --gzip DRR002308
2016-03-23T17:10:48 fastq-dump.2.4.4 err: item not found while constructing within virtual database module - the path 'DRR002308' cannot be opened as database or table
Error in job fastq_dump_paired while creating output files data/paired/DRR002308, data/paired/DRR002308/DRR002308_1.fastq.gz, data/paired/DRR002308/DRR002308_2.fastq.gz.
RuleException:
CalledProcessError in line 53 of /home/psturm/bears_analyses/Nikaido_2013_10.1101_gr.158105.113/Snakefile:
Command 'fastq-dump --split-files -O data/paired/DRR002308 --gzip DRR002308' returned non-zero exit status 3
Removing output files of failed job fastq_dump_paired since they might be corrupted:
data/paired/DRR002308
Will exit after finishing currently running jobs.
Exiting because a job execution failed. Look above for error message