Question: Raw Counts From Cufflinks Output
2
gravatar for Ge
6.3 years ago by
Ge80
Switzerland
Ge80 wrote:

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!

bedtools fpkm cufflinks counts • 6.5k views
ADD COMMENTlink modified 3.6 years ago by SmallChess480 • written 6.3 years ago by Ge80
0
gravatar for Istvan Albert
6.3 years ago by
Istvan Albert ♦♦ 80k
University Park, USA
Istvan Albert ♦♦ 80k wrote:

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.

ADD COMMENTlink written 6.3 years ago by Istvan Albert ♦♦ 80k
0
gravatar for Malachi Griffith
6.3 years ago by
Washington University School of Medicine, St. Louis, USA
Malachi Griffith17k wrote:

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.

ADD COMMENTlink written 6.3 years ago by Malachi Griffith17k
0
gravatar for SmallChess
3.6 years ago by
SmallChess480
Australia
SmallChess480 wrote:

It's not possible.

ADD COMMENTlink written 3.6 years ago by SmallChess480
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