Forum: Genomic Resequencing
04-05-2012, 08:08 AM
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Replies: 27
Views: 17,417
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Forum: Genomic Resequencing
04-05-2012, 07:38 AM
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Replies: 27
Views: 17,417
@jgibbons1
Both actually, it would be nice...
@jgibbons1
Both actually, it would be nice to have interpretable output where you can see how relevant a particular SNP is. Therefore, I was trying to get information such as; what gene it's from,...
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Forum: Genomic Resequencing
04-05-2012, 01:30 AM
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Replies: 27
Views: 17,417
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Forum: Bioinformatics
04-03-2012, 09:15 AM
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Replies: 5
Views: 3,619
I have the same problem
-- == statmap report...
I have the same problem
-- == statmap report ==
-- # single end (SE) reads: 0
-- # mapped SE reads: 0 (/ 0 = NA%)
-- # paired end (PE) reads: 30130376
-- # mapped PE reads: 28705774 (/...
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Forum: Bioinformatics
03-26-2012, 06:13 AM
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Replies: 2
Views: 4,268
Dear natstreet,
I'm currently wondering if...
Dear natstreet,
I'm currently wondering if this is a problem I'm having as my mate pair Illumina data is not assembling as all with Velvet, although soapdenovo seems to be working ok. Why would...
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Forum: Bioinformatics
02-28-2012, 02:33 AM
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Replies: 3
Views: 2,787
Back on this topic, is GATK ok to use for the...
Back on this topic, is GATK ok to use for the detection of prokaryotic SNPs with Illumina data? A lot of the information I'm reading refers to human data so I'm just worried I'd use it incorrectly. ...
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Forum: Bioinformatics
07-21-2011, 02:26 PM
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Replies: 3
Views: 1,713
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Forum: Bioinformatics
07-15-2011, 02:48 AM
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Replies: 3
Views: 1,713
extracted sequences from sff
Hi,
Has anyone successfully extracted a subset of sequences by their read ID from an sff file? I'm trying to separate plasmid and chromosomal reads from a bacterial sequencing project and I've...
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Forum: De novo discovery
03-07-2011, 04:38 AM
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Replies: 3
Views: 4,432
Coverage required for SNP detection?
Hi all,
I am sequencing bacterial genomes, certain genomic strains of which have been published but not the exact strains I'll be trying to detect SNPs for.
First off, as my title asks, can...
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Forum: Bioinformatics
02-21-2011, 09:28 AM
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Replies: 4
Views: 2,222
Was it shotgun or paired end/mate pair reads?...
Was it shotgun or paired end/mate pair reads? I've found that 8kb mate pair data on my 4.5Mb bacterial genome works wonders (5 scaffolds). This was done on a 1/4 plate.
Is your organism 7.5Mb and...
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Forum: Bioinformatics
02-21-2011, 04:11 AM
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Replies: 3
Views: 2,787
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Forum: Bioinformatics
02-21-2011, 03:21 AM
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Replies: 3
Views: 2,787
calling SNPs for prokaryotes
Hi,
I have genomic prokaryotic data and I want to look at SNPs between my data and the existing published data for very similar species. However, where MAQ worked well previously with Illumina...
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Forum: Bioinformatics
11-15-2010, 05:20 AM
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Replies: 11
Views: 12,275
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Forum: Bioinformatics
09-10-2010, 03:52 AM
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Replies: 1
Views: 2,745
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Forum: Bioinformatics
06-14-2010, 06:59 AM
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Replies: 8
Views: 3,773
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Forum: RNA Sequencing
04-26-2010, 01:40 PM
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Replies: 25
Views: 12,756
further issues
Dear all,
I'm still having a great deal of trouble with ERANGE. Whether I use paired end data or single read, I get the following error on the very last script of the runStandardAnalysis.sh...
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Forum: Bioinformatics
02-22-2010, 09:33 AM
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Replies: 47
Views: 30,558
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Forum: Bioinformatics
02-22-2010, 03:48 AM
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Replies: 47
Views: 30,558
Hi Cole,
Thanks for the new release! I've...
Hi Cole,
Thanks for the new release! I've been trying to use cuffdiff as described above. It runs for a while and then terminates as follows;
Importance sampling posterior distribution...
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Forum: RNA Sequencing
12-21-2009, 03:36 AM
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Replies: 25
Views: 12,756
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Forum: Bioinformatics
11-30-2009, 07:37 AM
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Replies: 3
Views: 2,596
same problem
Hi,
I have the same problem. Did Leo's solution work for you dukevn?
Thanks!
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Forum: RNA Sequencing
11-24-2009, 04:17 AM
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Replies: 9
Views: 4,974
spike sequences
Hi,
I am also wondering about the OP's question about spike sequences. They seem to be mentioned only in the ERANGE paper and online help files with no mention of what they actually are! Any...
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Forum: Bioinformatics
11-17-2009, 01:42 AM
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Replies: 11
Views: 5,102
same problem
Hi,
Was this problem resolved? I have a similar issue where I had 2 input files and the current ensembl reference genome (Homo_sapiens.GRCh37.56.gtf) but no references mapped and I only got 1...
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