Salmon or Kallisto without reference transcriptome - possible?
1
1
Entering edit mode
14 months ago
tanya_fiskur ▴ 50

Hello everyone,

Do I understand it correctly that if I want to count reads on a transcript level, and have only the mapped Illumina reads and a .gtf annotation file, I cannot use the Salmon or Kallisto? What could you recommend to use for this purpose?

Thank you!

next-gen • 560 views
ADD COMMENT
0
Entering edit mode

Hi,

I believe that you can use featureCounts: http://bioinf.wehi.edu.au/featureCounts/

I never use it, but from the description says that you need to provide a reference/genome GTF file and the mapped reads in sam/bam format.

I believe this answers your question,

António

ADD REPLY
0
Entering edit mode

FeatureCounts will assign reads to genes or exons, but I don't think it will assign to transcripts.

ADD REPLY
0
Entering edit mode

Yes, you're right!

This link explains that is not possible to get transcript-level quantification with featureCounts: A: How to get read counts on transcript level using featurecounts?

Sorry, for the bad answer and thank you for correcting me.

António

ADD REPLY
1
Entering edit mode
14 months ago

RSEM can assign reads by transcript.given a bam aligned to genome. You'll have to prepare the reference first, so you'll need the genome and gtf.

ADD COMMENT
0
Entering edit mode

Are you sure RSEM can now handle BAM files with genome alignments? Last time I used it it needed transcriptome alignments.

ADD REPLY
0
Entering edit mode

You might be right...I've always generated both, and run RSEM on that.

ADD REPLY
0
Entering edit mode

Right, you need the bam in transcriptomic coordinates. If you have that, you can already run salmon on it.

ADD REPLY

Login before adding your answer.

Traffic: 1118 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6