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Old 09-05-2013, 06:16 AM   #1
Location: Israel

Join Date: Oct 2012
Posts: 12
Default Count table from BAM file with custom gtf


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?

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Old 09-05-2013, 06:48 AM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

Yes, use htseq-count with the BAM file and the custom GTF file.
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Old 09-05-2013, 10:02 AM   #3
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Location: Gainesville

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you can also use bedtools if you want.
see here:
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Old 09-05-2013, 02:42 PM   #4
Wei Shi
Location: Australia

Join Date: Feb 2010
Posts: 235

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.
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