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Old 06-08-2016, 11:38 AM   #1
ronaldrcutler
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Default Tab delimited text files of gene counts

Hello all. I have merged .bam files containing count reads for each gene for each sample (biological replicate). I would get a tab delimited text file of gene counts that looks like this:

http://postimg.org/image/mlo85m08b/

I have been looking through how to do it in HTSeq but cannot find anything. Perhaps it can also be done in R?
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Old 06-08-2016, 12:10 PM   #2
GenoMax
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Use featureCounts. It is much faster. I will directly create the matrix of counts you need.
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Old 06-08-2016, 12:40 PM   #3
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Ok I'll try that out. Thanks
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Old 06-08-2016, 05:49 PM   #4
shi
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featureCounts is also available in Bioconductor R package Rsubread:

http://bioconductor.org/packages/rel.../Rsubread.html
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Old 06-17-2016, 08:37 AM   #5
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Also, I found that just opening the txt file in excel, modifying it there, and saving it as a tab delimited text file was quite easy.
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Old 06-17-2016, 08:50 AM   #6
GenoMax
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While excel has its uses you should be weary of using it to manipulate data files that will be used for some downstream application. See this: https://dontuseexcel.wordpress.com/2...ological-data/

Last edited by GenoMax; 06-17-2016 at 09:01 AM.
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Old 06-17-2016, 09:48 AM   #7
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Good Article, thanks for the heads up.
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