Question: counting after aligning miRNA reads to miRBase mature miRNA instead of reference genome
gravatar for inah
8 weeks ago by
inah10 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 • 125 views
ADD COMMENTlink modified 5 days ago by toralmanvar290 • written 8 weeks ago by inah10
gravatar for toralmanvar
5 days ago by
toralmanvar290 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 5 days ago by toralmanvar290
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