no gene expression for TNF if only count unique mapping

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4.7 years ago

xiyao.fei • 0

Hi I have a question about my RNA seq data. I use hisat2 to align the reads to hg19 genome, and use featureCounts to create gene count matrix. I just realize if no multimapping is allowed, all of my data has no unique gene mapping for TNF which should be one of the most common genes for tumor research. I assume it should have expressions but somehow I don't understand why there is none. If I choose multimapping in featureCounts, TNF has counts, which means all TNF reads have multimapping, which is not for sure belong to TNF. I wonder if anyone here have similar experience or provide me some suggestions. Thanks.

RNA-Seq • 593 views

ADD COMMENT • link 4.7 years ago by xiyao.fei • 0

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What is the read length, is this single or paired-end data?

ADD REPLY • link 4.7 years ago by ATpoint 82k

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Hi, the read length is 50, it is single end data.

ADD REPLY • link 4.7 years ago by xiyao.fei • 0

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