This is my command
$ minimap2 -t 4 -ax sr -p0 -N 6 -k 10 transciptome.fa reads.fastq > aligned_reads.sam
trancriptome.fa looks like this, it has more than 500 headers, I have added some here for example.
>12324_A TGCGGCCAATGTTTGTAATCAGCCCATAAATCCCAAGGAAATTTTGGGGAC >43354_B TGCGGCCAATGTTTGTAATCAGCGACCTAGGACCAAGGAAATTTTGGGGAC >42343_C TGCGGCCAATGTTTGTAATCAGGCGATTGTAACCAAGGAAATTTTGGGGAC >23435_D TGCGGCCAATGTTTGTAATCAGCACTTAGGAGCCAAGGAAATTTTGGGGAC
one of these transcript is mapped to one read in fastq but I expect multiple mapping.
Suppose, lets take Read 1 from fastq. Suppose it can match 1234_A and 43354_B but
I see in my .sam that it matches to only either one of them. I want to know all possible transcripts
matching a read.