Hi guys, I'm trying to move from HG19 to HG38. While running FeatureCounts using Refseq*.gtf I see some differences between HG19 and HG38. This I suppose is expected but I only would like to know if I'm doing wrong since I'm a newbie in the RNA-Seq HG38 analysis. Here some outputs of FeatureCounts for one sample (single end) as example:
Features : 460394
Meta-features : 24103
Chromosomes/contigs : 49
Total reads : 24944206.
Successfully assigned reads : 11116093 (44.6%)
The same sample with HG38:
Features : 536042
Meta-features : 50502
Chromosomes/contigs : 256
Total reads : 27605790
Successfully assigned reads : 6766947 (24.5%)
The alignment was performed using STAR and in both cases the Uniquely mapped reads % was around 93% or in any case it was comparable between the HG19 and HG38. Moreover, FeatureCounts was used as follows:
Fcounts <- featureCounts(files=fileName, annot.ext="/.../hg38.refseq.gtf", isGTFAnnotationFile=TRUE, GTF.attrType="gene_id", GTF.featureType="exon", nthreads=4, minMQS=3, isPairedEnd=FALSE)
Can anyone give me some feedback?
Thank you in advance