Short Read Aligner For A Particular Input Format

Question

[Nøke]

Hi colleges,

I have a csv-file which contains "reads \t readcount" lines. Is there a way to use Bowtie or BWA to map this sequences to my reference data, or is it necessary to reformat in some kind of fasta, for instance?

Thank for any advice.

Answer 1

[Jeremy Leipzig]

yes use a script to put this tsv into a fasta formatted file. you should store the counts in the deflines, since you might want to use that data to weight some quantitative analyses