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Forum: Bioinformatics 02-05-2017, 12:16 PM
Replies: 104
Views: 41,689
Posted By mcmc
Thanks. The data are from a metagenome with no...

Thanks. The data are from a metagenome with no good reference, so mapping to get error rates is not an option. My impression was that most(?) 2x250 HiSeq suffered from problems on the reverse read...
Forum: Bioinformatics 02-05-2017, 12:15 AM
Replies: 104
Views: 41,689
Posted By mcmc
Indeed, reducing it to -Xmx50g solved the problem...

Indeed, reducing it to -Xmx50g solved the problem (on a 64g exclusive node).

I've tried to improve my merging rate above ~75% and as you suspected I think poor quality is limiting the merging....
Forum: Bioinformatics 02-02-2017, 10:57 AM
Replies: 104
Views: 41,689
Posted By mcmc
I tried the command you suggested, and after...

I tried the command you suggested, and after first running out of memory (with -Xmx54g) and retrying with prealloc=t, now I get this error:

Initial size set to 19219231
Initial:
Ways=71,...
Forum: Bioinformatics 02-01-2017, 11:45 AM
Replies: 104
Views: 41,689
Posted By mcmc
Hi Brian, I have a very basic question about...

Hi Brian,
I have a very basic question about how merging works with the tadpole extend option. I have 2x250 HiSeq metagenome data, and about 75-80% of the reads merge by overlap after adapter...
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