I am trying to align miRNA sequencing reads (very short reads) to multiple fasta sequence reference(~150). I am expecting my reads to align separately against individual fasta sequences. To achieve this I am using SHRiMP aligner with the following command
SHRiMP_2_2_3/bin/gmapper-ls -N 2 -o 1 -E input.fasta ../reference.fasta > output.sam
The output consists of all reads that are mapped to the all the reference sequences, but each read is mapped only once. So assuming read1 maps against my 1st fasta reference sequence, then it will not report any hit against the other reference sequence.
Is there a way to achieve what I am trying to do?
I have also tried creating index file for my reference sequence and tried aligning using bowtie
bowtie index input.fastq > output
But, even this result in the read aligning only once with the reference.
Is there a parameter I can add to SHRiMP to obtain hits for individual fasta reference?