Raw read count to reference genes

[fanx]

I set a my own reference database containg selected genes (n=1500).
I had a 454 data about 100MB.

I run Bowtie 2 to get SAM, sorted/indexed. How do I get a excel-like raw read count output to each mapped reference gene? I mean simple count rather than expression study.

I noted there are some suggestion in the forum to use Bedtools or HTseq. Are they appropriate for solving my issue. If so, which performs better?

Thanks a lot.

[swbarnes2]

I set a my own reference database containg selected genes (n=1500).
I had a 454 data about 100MB.

I run Bowtie 2 to get SAM, sorted/indexed. How do I get a excel-like raw read count output to each mapped reference gene? I mean simple count rather than expression study.

I noted there are some suggestion in the forum to use Bedtools or HTseq. Are they appropriate for solving my issue. If so, which performs better?

Thanks a lot.

Try using BEDTools to intersect your .bam file with a .bed file with gene positions. Then you can process that with cut | uniq, or whatever.

[fanx]

swbarnes2: Thanks your suggestion. I did find BedTools has such a function. One thing to bother me is how to get coordinating Bed or GFF file. This is because I aligned my reads to NIH viral reference database for which only fasta and gbff are available for the download.

[eszter.ari]

Take a look at our read counter tool: http://seqanswers.com/forums/showthread.php?p=134850
https://code.google.com/p/recog/