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Why cufflinks does not report raw read count anymore? Which version of it do report?

Hi. I'm trying to get the read count by cufflinks, as I need the read count of each transcript so I can't use HTseq. I remember cufflinks used to report raw read counts. Can someone suggest me how can I get raw read counts by cufflinks?

rna-seq assembly cufflinks
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updated by Ram Ram • written by bibilong1111 • bibilong1111

3 answers

They aren't raw counts. Cufflinks computes expression in a probabilistic way to infer the read/transcript association.

If you can get reads out of cufflinks, they surely won't be "raw reads".

A tool like HTSlib will help you count things.

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written by karl.stamm karl.stamm

HTseq is a good tool for read count, cufflink only does differential expression analysis.

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written by madkitty madkitty

Although I'm not a big fan of Cufflinks, it can do a bit more. It computes based on some coverage-assumptions the read distribution per gene locus and assigns FPKM-values to the genes' transcripts.

I would not recommend trying to recompute the read counts from the FPKM values, since Cufflinks does some length normalisations of the transcripts as well as assigning multi-mapping reads.

However, I also recommend using HTSeq-count for getting the read-count.

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written by michael.ante michael.ante

Cufflinks is used for transcript assembly from aligned files. If you want to check whether distribution of reads over a co-ordinate support the gene model.

featureCount has served best for me to get read counts.

hth

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updated by Ram Ram • written by Manvendra Singh Manvendra Singh

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