Tab delimited text files of gene counts

[ronaldrcutler]

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?

[GenoMax]

Use featureCounts. It is much faster. I will directly create the matrix of counts you need.

[ronaldrcutler]

Ok I'll try that out. Thanks

[shi]

featureCounts is also available in Bioconductor R package Rsubread:

http://bioconductor.org/packages/release/bioc/html/Rsubread.html

[ronaldrcutler]

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.

[GenoMax]

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/

[ronaldrcutler]

Good Article, thanks for the heads up.