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  • 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:



    I have been looking through how to do it in HTSeq but cannot find anything. Perhaps it can also be done in R?

  • #2
    Use featureCounts. It is much faster. I will directly create the matrix of counts you need.

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    • #3
      Ok I'll try that out. Thanks

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      • #4
        featureCounts is also available in Bioconductor R package Rsubread:

        Alignment, quantification and analysis of RNA sequencing data (including both bulk RNA-seq and scRNA-seq) and DNA sequenicng data (including ATAC-seq, ChIP-seq, WGS, WES etc). Includes functionality for read mapping, read counting, SNP calling, structural variant detection and gene fusion discovery. Can be applied to all major sequencing techologies and to both short and long sequence reads.

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        • #5
          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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          • #6
            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, 08:01 AM.

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            • #7
              Good Article, thanks for the heads up.

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