BBSplit ambiguous dataset analysis

Question

[daewowo]

I have used bbsplit to split a metagenomic dataset into reads mapping to three genomes a, b, c.

bbsplit.sh in1={fastq_1} in2={fastq_2} ref={ref_str} ambiguous2=split basename={out_path}out_split_%.sam

If I want to identify which ambiguous reads align to 'a' and any other genome - is this only 'ambiguous_a'? or could 'ambiguous_b' and 'ambiguous_c' have reads that mapped to 'a' ie b&a and c&a?

Answer 1

[GenoMax]

Since you used split option for ambiguous2 following happens.

split   (write a copy to the AMBIGUOUS_ output for each reference to which it maps)

You may need to run combinations of a/b, b/c independently if you specifically need that information.