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Search: Posts Made By: Grammatonotus
Forum: Bioinformatics 02-21-2019, 05:26 PM
Replies: 219
Views: 69,142
Posted By Grammatonotus
a colleague suggests that the mapper may have...

a colleague suggests that the mapper may have come to a read that hits too many places in the reference. I have it set to place this at Random, would changing to First Best, None, or All be likely to...
Forum: Bioinformatics 02-21-2019, 03:47 PM
Replies: 219
Views: 69,142
Posted By Grammatonotus
When I run it locally about 52 Gb (I ran out of...

When I run it locally about 52 Gb (I ran out of system memory when I had it set to 58), on the cluster 439 Gb. I hope that's not the problem!
Forum: Bioinformatics 02-21-2019, 01:40 PM
Replies: 219
Views: 69,142
Posted By Grammatonotus
A little bit more information: the DNA sequence...

A little bit more information: the DNA sequence in the error message maps to the middle of a contig about 2.8 Mb, starts 402,000 bases in. I tried running this both locally and on a cluster and got...
Forum: Bioinformatics 02-21-2019, 01:06 PM
Replies: 219
Views: 69,142
Posted By Grammatonotus
shredding and mapping long reads to reference error

Hello,

I have a reference and I have an additional genome sequenced via 10x that contains 150k contigs from 1k to 7.5Mb. I am attempting to align the second to the first with BBMap by using the...
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