number of mismatches for the alignment

Question

[Sara]

I have Ribosome sequencing data and I want to align them. but I don't know how many mismatches must be considered in my command. do you know how many? if so why? thanks

[Pierre Lindenbaum]

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• Isolating reads from specific region from bam file
• identification of adapters from fastq file.
• read count normalization for spike
• M6A-seq and narrowpeak file
• error in macs2 usage
• filtering genes out from bam file using samtools

[Pierre Lindenbaum]

align with what ? what for ?which command ? http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002202

[Sara]

there is nothing here