Question: counting after aligning miRNA reads to miRBase mature miRNA instead of reference genome
gravatar for inah
17 months ago by
inah20 wrote:

I have human miRNA-seq data. In the past I have aligned these data using Bowtie2 to the reference genome (Homo_sapiens.GRCh38.dna.toplevel.fa), and I have subsequently performed counting using featureCounts with the annotation file hsa.gff3 from miRBase. . Now I have aligned the reads to the mature miRNA from miRBase (mature.fa), but when I look at the resulting bam files, the reads have a flag of 4 (segment unmapped) and there is no position information in mature.fa.

So can I use mature.fa as the reference for alignment and if so how is counting performed?

Thanks, Ina

mirna-seq • 748 views
ADD COMMENTlink modified 15 months ago by toralmanvar810 • written 17 months ago by inah20
gravatar for toralmanvar
15 months ago by
toralmanvar810 wrote:

yes, you can map the reads to mature miRNAs and can count the reads mapping onto it using samtools idxstat. Alternatively use can try using tool like mirdeep2 for complete analysis of miRNAs.

ADD COMMENTlink written 15 months ago by toralmanvar810
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 549 users visited in the last hour