In Salmon transcripts disappear. Sailfish doesn't allow bias correction in Galaxy.

[Tatiana Krutikhina]

Hello everyone,

I have an issue with aligners. I have a reference transcriptome (a long-read sequencing derived one), and illumina short-read sequencing data. I need to map the reads to reference transcriptome. I tried to do it with Salmon, first in Galaxy, and then in command-line version, and found out that some transcripts just disappered. They were just not present in the output.

I also tried Sailfish in Galaxy (Galaxy Version 0.10.1.1). It worked and transcripts didn't disappear, but if I added the length bias correction and GC bias correction, it output zero count file. Does it mean that the program works wrong? Can I trust Galaxy versions in general?

Thank you in advance.

Best regards,

Tanya

[Rob]

Hi Tanya,

  In general, we recommend using salmon instead of sailfish.

Regarding the problem of the transcripts disappearing; how many such transcripts vanished?  By default, salmon will collapse duplicate transcripts (transcripts with identical sequence) when indexing.  This results in only one from among the duplicate group being quantified.  The full information of what was collapsed (and what it was collapsed into) is retained in a file called `duplicate_clusters.tsv` in the index directory created by salmon.  This is a TSV file where the first column is the retained transcript (in the quant.sf file) and the second column is the transcript (identical) that was collapsed into it.  One retained transcript can have multiple duplicates.

Best,

Rob

[Anand]

I think this forum is no longer maintained

you need to use https://github.com/COMBINE-lab/salmon/issues

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Sailfish is available at https://github.com/kingsfordgroup/sailfish
Citation:
Patro, Rob, Stephen M. Mount, and Carl Kingsford. "Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms." Nature biotechnology 32.5 (2014): 462-464.
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[Anand]

i guess I am wrong 

Rob responded here 

I always use the GH issue tracker.