SoftClipped and Unmapped reads

[marieleoz]

Hi,

I am interested in exploring soft-clipped reads from some bam files I produced earlier using snippy, as a mean to identify insertion sequences. However, I'm not sure I can actually do this. Could you please help me figure out:

• what is the default value for --maxsoft? Looking at my bam files I guess it is 10 but the readme doesn't mention it (and I have too little experience with bam files to trust my guess).
• what happens to the reads that have >maxsoft bases that do not align? do they become Unmapped?
• does the bam file include the unmapped reads? The "Output files" table indicates that it does, but the "Unmapped Reads" section indicates that it doesn't. I am wondering whether the last reads in my bam file could be the unmapped ones, because the headers look like this: NB501755:180:HJLVNBGXB:4:23612:6187:5311 148 * 0 0 (then the sequence then 2 fields) instead of NB501755:180:HJLVNBGXB:1:13210:16123:16837 163 ctg.s1.000000F.arrow 1 60 7S144M = 140 290 (then the sequence, then 8 fields)

Thanks a lot! Marie