Cufflink, where is the raw gene count?
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4.2 years ago

Hey Guys, I need the raw count out of cuffquant, but all it provides is a binary file. It is really non-sense to run the tool for hours and yet get a useless file. I don't want to run cuffnorm to get the normalized gene counts I simply want the raw counts. Is it really not possible to generate with cufflink??

RNA-Seq quantification cufflink cuffquant • 2.9k views
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Ok, so basically, you mean no it is not possible.

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I think what he means is that if you need some specific data, then it's best to use a program that does exactly that and nothing else. featureCounts is very convenient and efficient and will deliver the counts within minutes.

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I edited your title. One question mark is perfectly sufficient.

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4.2 years ago

The TopHat2/Cufflinks pipeline is very powerful but you have to understand it well in order to make the most of it. I recently used it to de novo assemble a transcriptome and then fed the new transcriptome FASTA (produced by Cufflinks' gffread function) into Kallisto to calculate 'raw' read abundances over my original FASTQ samples.

Another option from the BAM output of TopHat2: HTSeq or featureCounts on your aligned: BAMs - A: How do you extract raw counts from CUFFLINKS?

Good luck Kevin

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3.2 years ago

just multiply by scaling factor: see Trapnell's answer here: https://github.com/cole-trapnell-lab/cufflinks/issues/12

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