Forum: Bioinformatics
06-19-2014, 01:26 PM
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Replies: 2
Views: 1,844
I finally determined the problem after a lot of...
I finally determined the problem after a lot of trial and error: MosaikJump writes a lot of stuff (29 Gb worth, indexing 2.6 Gbase of reference sequence) to /tmp. If /tmp doesn't have enough space,...
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Forum: Bioinformatics
06-09-2014, 08:44 AM
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Replies: 2
Views: 1,844
I found if I split up my reference set into...
I found if I split up my reference set into several smaller sets, MosaikJump won't stall.
But, instead, MosaikJump now crashes with a Segmentation fault. I allocated enough memory since it used...
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Forum: Bioinformatics
06-05-2014, 01:14 PM
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Replies: 2
Views: 1,844
MosaikJump stalls and does not complete
I am using Mosaik to align bacterial reads against a set of bacterial references sequences. I am having problems with hashing the references sequences with MosaikJump.
When I run
MosaikJump...
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Forum: De novo discovery
06-13-2012, 11:20 AM
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Replies: 36
Views: 24,870
Thanks for the info! I will give it a try.
...
Thanks for the info! I will give it a try.
I already created separate 454/Newbler and Illumina/SGA assemblies, and when I BLAT aligned the shorter Illumina/SGA scaffolds against the longer...
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Forum: De novo discovery
06-11-2012, 03:24 PM
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Replies: 36
Views: 24,870
Hi ians,
In your poster, you'd found that...
Hi ians,
In your poster, you'd found that for genomes >10Mb, it is better to pre-assemble the 454 reads, and then combine the 454 pre-assembled fragments with the Illumina reads for the final...
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Forum: Bioinformatics
08-03-2011, 02:48 PM
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Replies: 2
Views: 2,495
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Forum: Bioinformatics
04-04-2011, 10:09 AM
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Replies: 6
Views: 5,572
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Forum: Bioinformatics
04-01-2011, 12:51 PM
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Replies: 6
Views: 5,572
Good annotation editor?
I am seeking a good annotation editor. I have genes predicted by ab initio and RNA-seq gene/transcript predictors, but many of the predictions need to be fixed by hand. I am seeking an easy way to...
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Forum: Bioinformatics
03-07-2011, 03:57 PM
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Replies: 2
Views: 4,009
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Forum: Bioinformatics
03-03-2011, 11:22 AM
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Replies: 2
Views: 4,009
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Forum: Bioinformatics
11-10-2010, 12:00 PM
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Replies: 4
Views: 2,829
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Forum: Bioinformatics
11-09-2010, 12:30 PM
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Replies: 0
Views: 2,336
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Forum: Bioinformatics
10-28-2010, 09:45 AM
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Replies: 12
Views: 8,216
Thanks, kmcarr!
I had a similar problem: The...
Thanks, kmcarr!
I had a similar problem: The fragment length estimated by Cufflinks completely disagreed with that measured by the Agilent High Sensitivity Chip. But, subtracting 119bp from the...
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Forum: Bioinformatics
10-19-2010, 11:49 AM
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Replies: 12
Views: 8,216
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Forum: Bioinformatics
10-18-2010, 02:31 PM
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Replies: 12
Views: 8,216
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Forum: Illumina/Solexa
09-28-2010, 10:46 AM
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Replies: 4
Views: 12,645
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Forum: Illumina/Solexa
09-27-2010, 02:17 PM
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Replies: 4
Views: 12,645
Thanks much, kmcarr, for the info and for the...
Thanks much, kmcarr, for the info and for the speedy reply!
Out of curiosity, I took the final 32bp from each read, and ran them through FastQC. Indeed, the Overrepresented Sequences are Illumina...
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Forum: Illumina/Solexa
09-24-2010, 05:35 PM
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Replies: 4
Views: 12,645
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