featureCounts output has letters and +/- sign

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2.3 years ago

mgranada3 ▴ 30

Hello, I have created a featureCounts table and 10 of my files had weird outputs. Some values were my organism name and others were a "+" or "-". I could not find anything about this in the manual. I tried to re-run featureCounts and got the same problem. I also tried to run featureCounts on the .sam files and got the same results. This is giving me problems when trying to run Deseq2 in R.

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rnaseq featurecounts deseq2 • 1.1k views

ADD COMMENT • link 2.3 years ago by mgranada3 ▴ 30

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I don't think this is a featureCounts error. I would guess that columns in your GTF/GFF file are not what they should be, or something went wrong during mapping. It appears that gene names and/or strands are picked up during counting.

ADD REPLY • link 2.3 years ago by Mensur Dlakic ★ 27k

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Thats so weird because I used the same GTF file for everything. I will look into this. Thanks

ADD REPLY • link 2.3 years ago by mgranada3 ▴ 30

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Can you load that into R and confirm presence of these symbols in the object? Just to exclude an Excel-ish formatting error. Has this file been manipulated somehow?

ADD REPLY • link 2.3 years ago by ATpoint 81k

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So I think my files got corrupted because when I re-ran HISAT2 for my alignment and then used featurecounts again I got the same values but now no letters or +/- signs.

ADD REPLY • link 2.3 years ago by mgranada3 ▴ 30

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