Is it possible to only view soft clipped bases where in the current window not all of the bases for that read are soft clipped? I'm working with somatic SVs in ONT reads and the screen is full of reads that are fully soft clipped - it makes it very hard to focus on the few where...
For usage, typematchclipsand return. The default parameters should be good for most current platforms as of 2013. If your reads are longer than 200 bases or the read quality is low, change maximum allowed mismatched bases to 2 or 3 with option-me. ...
I am looking at whole genome sequencing DNA data and interested in insertions such as LINE1 retrotransposons or viruses. I would like to have a way to get rid of all of the reads which do not have soft-clipped segments, to be left with o...
poor quality bases (mismatches only make the alignment score worse) structural variation in your sample compared to the reference reads overlapping the start and end of contigs (including circular genomes) Read aligners output a SAM file. Column 6 in this format stores the CIGAR string. which de...