Question: salmon gene quant to DESeq2
0
gravatar for matthew.johnson
8 days ago by
matthew.johnson10 wrote:

Hi again - I successfully ran salmon on my fastq files, including gene-level summary via a simple two-column map file of transcript-to-gene-ID. This gives me an output like this for each fastq:

Name    Length  EffectiveLength TPM NumReads
ENSMUSG00000114165  2016    1815.57 0.0732938   3.29409

I tried simply passing these outputs on as input to DESeq2 for differential expression, selecting under input "TPM values (e.g. from sailfish or salmon)", then for Gene mapping format selecting "Transcript-ID and Gene-ID mapping file" and specifying the same two-column table used for the salmon runs (haha).

I got this vague error:

Fatal error: An undefined error occurred, please check your input carefully and contact your administrator.
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
  line 2 did not have 6 elements
Calls: read.table -> scan

So, not sure where the problem's arising, but for starters, the salmon output contains both TPM and NumReads (i.e., I presume, a read count estimate). Do I need to extract one or the other of these columns to pass on to DESeq2? And also, is the transcript-to-gene map even necessary for DESeq2 since the gene-level summary has already been done by salmon?

Thanks so much for your help!

rna-seq galaxy • 37 views
ADD COMMENTlink written 8 days ago by matthew.johnson10
0
gravatar for Jennifer Hillman Jackson
8 days ago by
United States
Jennifer Hillman Jackson22k wrote:

Hello - I haven't seen this before but have mostly worked with count input (not TMP). The tutorials for Deseq also use count inputs. https://galaxyproject.org/tutorials/nt_rnaseq/#analysis-of-the-differential-gene-expression & http://galaxyproject.github.io/training-material/topics/transcriptomics/

Are you working at Galaxy Main (http://usegalaxy.org)? We would like to look at the exact usage and parameters to test if this option has a bug - or to help clarify usage - and sharing a history link or sending in a bug report is the most direct way to do that. How to: https://galaxyproject.org/issues/#usage-problem-reporting Please be sure to leave the datasets undeleted and include a link to this post so we can associate the two.

Others are still welcome to reply if they understand your use case from the given information.

Jen, Galaxy team

ADD COMMENTlink written 8 days ago by Jennifer Hillman Jackson22k

I didn't see a bug report sent in yet, but you can still do that if usage problems are still present.

ADD REPLYlink written 5 days ago by Jennifer Hillman Jackson22k
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