FeatureCounts (Ensembl based GTF v.s In-built Entrez GTF) variances in count data

Hi everyone

Firstly thank you in advance for any help you can give, I am new to bioinformatics and biostars has been immensely helpful. I have human RNA-seq data that I am currently processing, I've gone through my trimming and aligning (with STAR) stages and have just used featureCounts to counts in my data.

I have tried two different methods for featureCounts both worked but varied in their count data. Firstly I used the HG38 GTF from ensembl and secondly I used the built in HG38 GTF from the RSubread package, (entrez gene)...

Both were successful but I compared corresponding genes between ensembl and entrez gene and the count data was quite different - Total number of reads also differed from 36165730 to 38752850 respectively.

Why would the total number of counts be higher in the case of entrez gene? - Seems strange considering ensemble is larger in scope.

I understand that ensembl and entrez do not completely align but the differences seemed quite dramatic, Is this normal? and if I use the entrez values is this okay considering I aligned my data using an ensmbl GTF.

featurecounts rna-seq sequencing

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updated 3.2 years ago by Ram

• written 5.9 years ago by harrydolan.dc •

I think you might find the following manuscript helpful: A comprehensive evaluation of ensembl, RefSeq, and UCSC annotations in the context of RNA-seq read mapping and gene quantification

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written 5.9 years ago by newbio17

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