khuang28jhu
khuang28jhu
Hey man, Thanks for the comment. I am currently updating/re-organizing the RRBS part of the pipeline. I pulled that part down and that's why the code just exited. Sorry for...
Can you give me more context? The commands you used, the genome you matched to...etc and whether you tried the example test case and if it worked and your version...
Would you mind sharing with me the data you are using, because I can not reproduce the error with the command you are using on my test data.
1) Did the toy example work? If yes, [Does this help?](https://github.com/khuang28jhu/bs3/issues/5) 2) Maybe try increasing the -m NO_MISMATCHES or -K ALIGNMENT LENGTH number ?
Can you show the the exact process (**exact screen printout and command**) when you **run the toy example from start to finish**?
So the toy example Does work then [does this help?](https://github.com/khuang28jhu/bs3/issues/5)
It's an not-official version that they released that fixed one of pair-ended matching bug
From above, "Total Reads Aligned, MAPQ >= 10 Aligned, MAPQ < 10 Unaligned Too Short/Too Many Ns %Pairs Reads/s Time in Aligner (s) 6,400,000 0 (0.00%) 0 (0.00%) 0 (0.00%)...
The seed length of 20 is too large for read length around 50. In general, at least for SNAP is concerned, the seed length of these hash-based methods should be...
Thanks for the comment. Will update accordingly.