Question: FPKM values all 0 from Stringtie
0
gravatar for jammydodger123456
3.1 years ago by
jammydodger12345630 wrote:

I have analysed a few studies from the species Schistosoma mansoni using HISAT2 and Stringtie, mostly with no problems, using the genome and corresponding annotations retrieved from the same site (http://parasite.wormbase.org/Schistosoma_mansoni_prjea36577/Info/Index). I have seen people discuss this same problem due to getting the genome and annotations from different sites (ie they aren't compatible), but this surely isn't the case here.

Studies analysed are from 2012-2015. Attempted analyses of two more recent studies (both 2016) have resulted in the columns; Coverage, FPKM and TPM all containing 0s in every single row.

I only want to obtain FPKMs for existing genes, so I am using Stringtie with no new transcript assembly. My command is as follows;

stringtie -p 8 -G ../SmanAnnos.gtf -e S24_B1.bam -A S24_B1.tab

I'm a bit of a noob to Stringtie, so the more simple the explanation the better. Many thanks.

rna-seq stringtie • 970 views
ADD COMMENTlink written 3.1 years ago by jammydodger12345630

It's possible that the contig names in SmanAnnos.gtf don't match those that were used in the reference genome FASTA that you used to produce your BAMs.

From where did you obtain SmanAnnos.gtf and which reference genome did you use? Are they from the same source?

ADD REPLYlink written 3.1 years ago by Kevin Blighe71k

Yes, the annotations and genome are from the same source. I don't understand why this hasn't worked, as I had previously analysed transcriptomic data for this species using the same genome and annotation files and this problem didn't happen before.

ADD REPLYlink written 3.1 years ago by jammydodger12345630
1

Just to pacify me, can you try:

stringtie S24_B1.bam -p 8 -G ../SmanAnnos.gtf -e -A S24_B1.tab

If that does not work, try

stringtie S24_B1.bam -p 8 -A S24_B1.tab
ADD REPLYlink written 3.1 years ago by Kevin Blighe71k

Your first command suggestion worked. Thank you very much Kevin!

ADD REPLYlink written 3.1 years ago by jammydodger12345630

Great - glad to have helped

ADD REPLYlink written 3.1 years ago by Kevin Blighe71k
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