Comments (4)
Hi Alexandre,
It seem that v01 give you a better assembly result (N50 165 vs 103Kb), but did you change some parameters to accomodate the low long-read coverage (5X)?. You shold probably set the -N parameter to -N 2. Can you count the number of deleted edges at the liger step for each assembly ("grep DELETED *liger.log")?. Overall, there are few differents between v01 and v02 involving the WenganD pipeline, thus results might be similar with V02 a bit more accurate.
Best,
Alex
from wengan.
Hi,
Thanks for the rapid answer!
I have 494 (v01) vs 14956 (v02) deleted edges (grep DELETED *.ligerlog | wc -l) for each assembly. So I guess I am loosing quite a lot of information in v02 here?
Indeed, I had -N 2 for the v01 but not for the v02. I am running v02 again with the N parameter included this time. I will let you know the results when it's finished, in a couple of days probably.
Cheers,
Alexandre
from wengan.
Hi,
Some updates, as promised. Indeed, when adding the -N 2 parameters, results are extremely similar between v01 and v02, even though some slight differences appear.
Thanks a lot!
Alexandre
from wengan.
Great!
Best,
Alex
from wengan.
Related Issues (20)
- Error 139 HOT 4
- Setting new tmp directory for intermediate files HOT 1
- error2 HOT 3
- asm1.minia.41.contigs.fa] Error 127 HOT 3
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- Using error corrected long reads HOT 2
- Error 137 HOT 4
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- unrecognized command 'iupac2bases'. Abort! HOT 1
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- SPolished.asm.wengan.fasta] Error 136 HOT 3
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