As I understand it, the mapper.pl aspect of miRDeep2 will aim to map reads to the genome of interest with the help of bowtie, but not based on any structural signitures of a miRNA. These (5,776,111) reads are later filtered based on miRNA characteristics, giving those that look like miRNAs (3,265,557), and those that don't (2,510,554)
I would like to extract these 2,510,554 reads for further analysis (ie attempting to map against an index of other smRNA species). Is there any way to do this?
miRDeep2.pl relevant readout below
Converting input files
building bowtie index
mapping mature sequences against index
mapping read sequences against index
Mapping statistics
#desc total mapped unmapped %mapped %unmapped
total: 5776111 3265557 2510554 56.536 43.464
Dog: 5776111 3265557 2510554 56.536 43.464
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jammydodger123456 •
You could manually run bowtie and collect unmapped reads as noted in answers here --> Separate unaligned reads in fastq format using bowtie
Yes but surely at the point of determining reads according to miRNA characteristics, this is past any bowtie mapping?
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