Question

Best Programs for transcript counts

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6.9 years ago

oma219 ▴ 40

Hello, I just finished producing gene counts and I was going to move into transcript counts. I think featureCounts and cufflinks are able to do transcript counts but I just wanted to get other opinions on programs they found to useful when it came to producing transcript counts? Thanks.

sequence rna-seq • 1.7k views

ADD COMMENT • link updated 6.9 years ago by Carlos Caicedo ▴ 210 • written 6.9 years ago by oma219 ▴ 40

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Currently, probably Salmon or Kallisto are the best programs. RSEM and eXpress are good choices. Stringtie is Cufflinks replacement. Lastly, I think featureCounts is not good for transcript counts, as it will discard too many "multi-mapping" reads.

ADD REPLY • link 6.9 years ago by h.mon 35k

score 1 · Answer 1 · 2017-06-01

RNA-skim is another alternative that use a different approach. It partitions the transcriptome into disjoint transcript clusters based on sequence similarity and introduces the notion of sig-mers that are a special type of k-mers uniquely associated with each cluster. It was developed for RNA-Seq quantification at transcript level.