I have around 12,000 smallRNA reads (sequences) for which I need to find the total mapped reads for EACH individual sequence. They are in a collapsed fasta file ensuring the sequences appear only once in the entire file (trimming and quiality filtering etc have been already done ). I want to know the total number of reads ( counts) for each sequence, meaning if sequence A maps to multiple places- I will need the output for the total number of mapped reads for sequence A and so on.... Eventually I want to generate an expression profile for these sequences ( may be the top 50 ). I had previously used miRdeep2 tool and the quantifier.pl script for that suite was very helpful at that time. However these are not miRNAs and so miRdeep2 cannot be used here.
I can map these to the reference genome and generate a BAM file. But will samtools be of help in this situation ? I am a bit confused. Any help is most appreciated.