Number of reads mapped with each sequence in a multiple reference sequences

Question

[KT]

Hi all,

I have single-end reads and my aim is to map all the reads with multiple reference sequences in one FASTA file. These reference sequences are on the same gene location but they contain different variants. Does anyone know how I can enumerate the number of reads mapped with each sequence in my reference sequence list? Many thanks.

[natasha.sernova]

Is it what you need?

Extracting reads mapped to any of multiple references

[GenoMax]

Depending on how many differences there are in the reads and the reference and the fact that most reads are going to multi-map (which you would need to adjust settings for with an NGS aligner) this may require some trial and error to come up with settings that will work.

See this thread for ideas: bwa mem perfectly align reads over their entire length

[Devon Ryan]

This sounds like an ideal use-case for Salmon or Kallisto.