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

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

Hi,

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?

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

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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
crazyhottommy
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you can also use bedtools if you want.
see here:
http://genomespot.blogspot.com/2013/...ix-part-1.html
http://genomespot.blogspot.com/2013/...ix-part-2.html
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Old 09-05-2013, 02:42 PM   #4
shi
Wei Shi
 
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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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