HISAT2 soft-clipping default settings

usegalaxy.org.au support
1

Hello,
I had a question about the default settings for HISAT2 on Galaxy, and whether soft-clipping is applied? Normally HISAT2 applies soft-clipping but I’m unsure of whether this is the case on Galaxy. As I haven’t trimmed for adaptor sequences, I am wanting to ensure that soft-clipping is applied. I can see for HISAT2, if you select ‘Advanced Settings’ you can choose whether soft-clipping is applied under Scoring Options, does this mean by default (e.g. not using any advanced options) it is not applied?

Thanks in advance.

2

Hi @clarissa
I believe HiSAT2 uses soft clipping with the default settings, but please check any BAM file. Soft clipping is recorded in CIGAR (column 6) with S character. It is very common, especially if you not trimmed for adapter.
Hope that helps.
Kind regards,
Igor

3

Thanks for your reply @igor. I have checked the CIGAR column and most of them end in the character ‘M’, however some of them also end in ‘S’. Does that mean I can assume soft clipping was used?

4

Hi @clarissa
yes, presence of S means soft clipping was used. It is used only for reads with soft clipped nucleotides. M means match, well, match or mis-match, to be precise. You can check description of CIGAR string in SAM/BAM documentation.
Kind regards,
Igor

1 Like