Open slbai01 opened 1 year ago
Is there a reason you change the default k and w values for index?
For the TLEN issue, @mourisl can you take a look when you get time? Thanks!
The genome is too large, and the default parameters can't complete the index. #9 has described this question.
Hi @slbai01, sorry for the delayed reply. The TLEN issue could be due to the data type overflow. I have pushed an updates to the li_dev5 branch, could you please checkout that branch and give it a try? I think the split-alignment mode of Hi-C data, the sign of TLEN does not make much sense, and the length may be off by the read length depending on the strand. But at least, now the value of TLEN is reasonable.
I am running
chromap: 0.2.5-r473
on a highly repetitive genome, but theTLEN
information in the sam file looks wrong.Since only one best match is output by default, I suspect that some errors in handling multiple matches result in no output of the read matching information corresponding to
TLEN
.Below is the information about several pairs of reads.
command line: