Question: htseq-count results in missing genes
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gravatar for YOUSEUFS
2.2 years ago by
YOUSEUFS10
YOUSEUFS10 wrote:

Hello Bioinformatics wizards!

I've recently counted my aligned reads w/ htseq-count and I am now placing them in excel next to their PROKKA gene ID's to see what genes these reads are actually aligning to. I'm noticing that out of the 1080 genes 37 of them are missing in my htseq-counts. Genes with 0 counts still show up. Is this to be expected? Have I fudged up somewhere? knowledge please!

Many thanks, bioinformatics peon

rna-seq htseq-count • 679 views
ADD COMMENTlink written 2.2 years ago by YOUSEUFS10

Does the gtf contain those genes?

ADD REPLYlink written 2.2 years ago by WouterDeCoster41k
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