This is a somewhat already discussed argument but I'm wondering if I'm missing something...the "usual" way after having done a tophat/[cufflinks]/cuffdiff analysis is restarting from the .bam files and generate raw counts for deseq with tools like htseq.
I would like to save up on CPU cycles and I'm wondering if the "Count tracking files" found in the cuffdiff output could be the solution, the documentations states that they contain " Gene counts. Tracks the summed counts of transcripts sharing each gene_id" and I believe that these could work to generate input counts for DeSeq, even if the criteria to assign a read to a transcript will be different from the htseq ones.
I would like to save up on CPU cycles and I'm wondering if the "Count tracking files" found in the cuffdiff output could be the solution, the documentations states that they contain " Gene counts. Tracks the summed counts of transcripts sharing each gene_id" and I believe that these could work to generate input counts for DeSeq, even if the criteria to assign a read to a transcript will be different from the htseq ones.