Raw Counts From Cufflinks Output

Question

[Ge]

Hi, I want to ask how to get the raw counts from the output of cufflinks. One way to do this is to use the fpkm.

raw counts = FPKM * (length of that transcript/1000) * (# of mapped reads / 1e6)

The FPKM and length of transcript are in the cufflinks FPKM Tracking Files. But how about the # of mapped reads?

For instance, we have a foo.bam. samtools view -c (-f|-F) flag foo.bam can do this job but I am not quite which flag should I set when it's single-end or paired-end.

Thanks!

Answer 1

[Istvan Albert]

A workaround could be to get the number reads that overlap with an interval via bedtools or bedops something like:

bedtools intersect -c ...

and use the reads file and the transcript interval file. The -c flag can give you counts that overlap.

Answer 2

[Malachi Griffith]

A workaround could also be to get the number of reads for all genes/transcripts specified in a GTF/GFF file using htseq-count

htseq-count [options] <sam_file> <gff_file>

Download and install and usage instructions.

Answer 3

[scchess]

It's not possible.