Forum: Illumina/Solexa
08-02-2012, 01:55 PM
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Replies: 83
Views: 29,115
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Forum: Bioinformatics
07-19-2012, 07:47 AM
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Replies: 3
Views: 2,522
454 may be a better platform if you need more...
454 may be a better platform if you need more bases.
it will be difficult to de novo assemble all your amplicons given that they are very similar. For the ones you do know, you could align reads...
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Forum: Bioinformatics
07-13-2012, 07:50 AM
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Replies: 16
Views: 7,844
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Forum: Bioinformatics
07-13-2012, 07:47 AM
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Replies: 24
Views: 14,889
For me it was pretty systematic.
My solution...
For me it was pretty systematic.
My solution seems to work thus far as I have rerun 3 samples that previously failed.
I think the problem may stem from when Cufflinks' threads are competing at...
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Forum: The Pipeline
07-12-2012, 11:27 AM
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Replies: 104
Views: 147,799
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Forum: De novo discovery
07-10-2012, 09:57 AM
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Replies: 36
Views: 24,844
Yeah the documentation is a bit rough. This...
Yeah the documentation is a bit rough. This manual (https://wiki.umiacs.umd.edu/cbcb/images/9/99/SOAPdenovo-V1.05.manual.txt) is a bit better.
You're doing a fungus right? How much sequence...
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Forum: De novo discovery
07-10-2012, 08:36 AM
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Replies: 36
Views: 24,844
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Forum: De novo discovery
07-10-2012, 07:51 AM
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Replies: 36
Views: 24,844
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Forum: Bioinformatics
07-09-2012, 09:24 AM
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Replies: 2
Views: 1,780
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Forum: Bioinformatics
07-09-2012, 09:11 AM
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Replies: 16
Views: 7,844
I've seen the "too many open files" error when...
I've seen the "too many open files" error when dealing with alignments else where. I've seen this when sorting very large bam files. This ultimately happens when samtools tries merging all the...
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Forum: Bioinformatics
07-09-2012, 09:03 AM
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Replies: 24
Views: 14,889
Solved?
I ran a test run over the weekend using data that had failed before. The run was successful over the weekend!
I ran with just as many threads as the box has. This contrasts with the pervious failed...
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Forum: Bioinformatics
07-06-2012, 02:19 PM
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Replies: 4
Views: 1,618
For SNP calling, there's not really much reason...
For SNP calling, there's not really much reason to go past 50bp in length. Especially when comparing to 2x150 bp reads, you'll theoretically have 6x more sampling per basepair with the smaller single...
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Forum: Bioinformatics
07-06-2012, 09:46 AM
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Replies: 24
Views: 14,889
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Forum: Bioinformatics
07-03-2012, 11:02 AM
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Replies: 24
Views: 14,889
I found the segment_juncs command that died in...
I found the segment_juncs command that died in runs.log.
I tried rerunning the exact command, but with p=1 (singlethreaded), and get the same error.
I've dug through the source of reads.cpp to...
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Forum: Bioinformatics
07-03-2012, 09:57 AM
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Replies: 24
Views: 14,889
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Forum: De novo discovery
06-15-2012, 08:42 AM
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Replies: 36
Views: 24,844
That's pretty dope. I definitely need to try...
That's pretty dope. I definitely need to try this.
I'm curious, did you choose 400bp because you didn't sequence with FLX+? I would think that larger frags would be advantageous.
Yeah, in...
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Forum: De novo discovery
06-13-2012, 03:32 PM
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Replies: 36
Views: 24,844
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Forum: De novo discovery
06-13-2012, 09:36 AM
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Replies: 36
Views: 24,844
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Forum: Illumina/Solexa
06-05-2012, 07:57 AM
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Replies: 83
Views: 29,115
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Forum: Illumina/Solexa
06-04-2012, 09:18 AM
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Replies: 83
Views: 29,115
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Forum: Bioinformatics
06-04-2012, 08:46 AM
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Replies: 17
Views: 10,696
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Forum: Bioinformatics
06-04-2012, 07:54 AM
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Replies: 17
Views: 10,696
Be careful here. Most assemblers do not look at...
Be careful here. Most assemblers do not look at header information to establish pairs. Rather, the 1st read in file a is paired with the 1st read in file b. If you remove any reads, be sure you also...
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Forum: De novo discovery
05-30-2012, 07:37 AM
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Replies: 9
Views: 3,464
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Forum: Bioinformatics
05-30-2012, 07:31 AM
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Replies: 4
Views: 1,811
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Forum: Bioinformatics
05-30-2012, 07:26 AM
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Replies: 4
Views: 1,719
Poni,
Likely the issue isn't that it is...
Poni,
Likely the issue isn't that it is diploid, but rather you just have a much more complex organism (which is often the case of diploid organisms.) The assembler doesn't really care as it will...
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