I have ULont reads mapped to draft assembly and would like to extract reads that span two contigs at ends/beginings. Read1 from the below example image.
Soft clipping information from the CIGAR can be used to identify such reads but is a tool or any easy way to extract such reads?
any help is much appreciated. thank you
Thank you. It was an example image. I have multi-contig file (~19k) which is not feasible to check this way. I want to extract reads that span any 2 contigs, something like reads supporting translocations but in my case I want the reads that spans either beginning or ends
hum... why ?
If I'm understanding correctly, the "spanning" reads need not be between adjacent contigs, so (19000 choose 2) of the above commands would need to be executed. This, of course, could be offloaded to a script.