Forum: General
12-11-2018, 08:20 AM
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Replies: 1
Views: 611
diagnostics labs - what do they use?
Hi all, just wondering what the current state-of-play is with regards to clinical diagnostics labs, whether in the UK, European, or US context. Are small gene panels still the go-to? Or are more...
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Forum: Bioinformatics
09-04-2012, 06:32 AM
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Replies: 7
Views: 4,372
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Forum: Bioinformatics
08-02-2012, 07:54 AM
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Replies: 7
Views: 4,372
Hi dkoboldt,
I've just started using VarScan...
Hi dkoboldt,
I've just started using VarScan (v2.2.11) and so far am very happy with what it can do. I am formatting my output from mpilup2snp and mpileup2indel as VCF, but, for me at least, the...
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Forum: Bioinformatics
04-11-2012, 06:04 AM
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Replies: 5
Views: 5,633
Hi earonesty,
thanks for the link. I couldn't...
Hi earonesty,
thanks for the link. I couldn't get the patch to apply (though admittedly I'm not experienced with doing so). Is the command much different to "patch bowtie bowtie-gzip.patch" ?
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Forum: Bioinformatics
11-24-2011, 06:39 AM
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Replies: 138
Views: 61,532
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Forum: Bioinformatics
11-24-2011, 06:17 AM
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Replies: 138
Views: 61,532
In following the workflow mentioned above, I've...
In following the workflow mentioned above, I've come up against an error, and I'm wondering if I'm alone in this. Has anyone experienced difficulty with using CountCovariates tool, specifically with...
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Forum: Bioinformatics
05-04-2011, 02:32 AM
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Replies: 48
Views: 57,958
Hi ketan,
thanks for your fast response!...
Hi ketan,
thanks for your fast response! Unfortunately the AF1 tag is not very informative to me, as it's only for the first ALT allele, and pretty much always 1.0 or 0.5. The AF tag, as I...
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Forum: Bioinformatics
05-03-2011, 11:54 AM
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Replies: 48
Views: 57,958
Hi,
At the risk of appearing quite dumb, if...
Hi,
At the risk of appearing quite dumb, if anyone can help with (admittedly my first day using) the vcf format and vcftools, I'd be very grateful! For reference, I'm using illumina reads,...
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Forum: De novo discovery
11-17-2010, 07:29 AM
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Replies: 58
Views: 40,880
In terms of the practical memory limitations...
In terms of the practical memory limitations faced by Velvet, how big/complex a transcriptome can likely be assembled using Oases? I understand Curtain was brought out to get around the memory issues...
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Forum: Bioinformatics
06-28-2010, 06:08 AM
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Replies: 46
Views: 25,905
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Forum: Bioinformatics
06-28-2010, 04:36 AM
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Replies: 12
Views: 6,022
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Forum: Bioinformatics
05-18-2010, 01:44 AM
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Replies: 15
Views: 9,507
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Forum: De novo discovery
05-17-2010, 05:20 AM
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Replies: 82
Views: 44,354
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Forum: Bioinformatics
05-14-2010, 03:08 AM
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Replies: 8
Views: 3,261
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Forum: RNA Sequencing
05-13-2010, 08:52 AM
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Replies: 11
Views: 5,067
I have a situation where I initially have two...
I have a situation where I initially have two main groups (four replicate organisms in each), so that is pretty straightforward. However I would also like to do some within-group comparisons too -...
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Forum: Bioinformatics
05-13-2010, 08:28 AM
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Replies: 8
Views: 3,261
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Forum: Illumina/Solexa
05-13-2010, 03:06 AM
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Replies: 5
Views: 4,519
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Forum: Bioinformatics
05-04-2010, 08:50 AM
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Replies: 46
Views: 25,905
Hi Simon,
this sounds like a very simple...
Hi Simon,
this sounds like a very simple question, but I have to ask anyway...
The gene counts file in the DESeq vignette gives one gene count per gene, per lane, or seems to at least. Can I...
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Forum: RNA Sequencing
03-16-2010, 04:08 AM
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Replies: 11
Views: 5,067
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Forum: Bioinformatics
03-04-2010, 07:28 AM
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Replies: 47
Views: 26,266
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