Count table from BAM file with custom gtf

[tamari]

Hi,

I have an aligned (not by me) BAM files and I need to get eventually count table (for DESeq and EdgeR) the problem is the following: I neet to find the counts against a custom gtf file which contains more possible transcrips that were used by the preson who created the data (predicted LINCs mainly). What I do is transfer BAM to fastq, use RSEM to realign with the custom gtf and only then get the count table,

My question; is there a way to get the count table against the gtf file without the fastq transform and the relignment?

Thanks!!!
tamari

[dpryan]

Yes, use htseq-count with the BAM file and the custom GTF file.

[crazyhottommy]

you can also use bedtools if you want.
see here:

http://genomespot.blogspot.com/2013/06/generate-rna-seq-count-matrix-part-1.html

http://genomespot.blogspot.com/2013/06/generate-rna-seq-count-matrix-part-2.html

[shi]

You may use the featureCounts program included in the Subread pacakge. It is a very fast read counting program, counting 10 million reads in just 3 minutes.