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Salmon or Kallisto without reference transcriptome - possible?

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
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updated by swbarnes2 swbarnes2 • written by tanya_fiskur • tanya_fiskur

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

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written by antonioggsousa antonioggsousa

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

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written by swbarnes2 swbarnes2

1 answer

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.

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written by swbarnes2 swbarnes2

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

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written by Devon Ryan Devon Ryan

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

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written by swbarnes2 swbarnes2

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

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written by Rob Rob

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