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Old 10-26-2012, 08:15 PM   #1
fanx
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Default Raw read count to reference genes

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.
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Old 10-27-2012, 03:23 PM   #2
swbarnes2
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Quote:
Originally Posted by fanx View Post
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.
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Old 10-30-2012, 10:51 PM   #3
fanx
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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.
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Old 04-11-2014, 05:34 AM   #4
eszter.ari
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Take a look at our read counter tool: http://seqanswers.com/forums/showthread.php?p=134850
https://code.google.com/p/recog/
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