Raw read count to reference genes

fanx · 10-26-2012, 08:15 PM

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 · 10-27-2012, 03:23 PM

Quote:

Originally Posted by 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.

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 · 10-30-2012, 10:51 PM

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 · 04-11-2014, 05:34 AM

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

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Raw read count for RN-seq	usagi	Bioinformatics	5	04-13-2014 04:11 PM
Extracting reads with highest identity to my genes of interest from illumina raw data	ataheri	Bioinformatics	5	07-25-2012 12:33 AM
multiBamCov or htseq-count to count read per feature ?	NicoBxl	Bioinformatics	1	07-03-2012 03:05 AM
Cuffdiff results for genes with low count for one treatment	pinin4fjords	Bioinformatics	2	10-18-2011 02:10 AM

10-26-2012, 08:15 PM	#1
fanx Member Location: USA Join Date: Sep 2012 Posts: 22	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.

10-30-2012, 10:51 PM	#3
fanx Member Location: USA Join Date: Sep 2012 Posts: 22	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.

04-11-2014, 05:34 AM	#4
eszter.ari Junior Member Location: Vienna Join Date: Dec 2012 Posts: 8	Take a look at our read counter tool: http://seqanswers.com/forums/showthread.php?p=134850 https://code.google.com/p/recog/