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Forum: General 12-11-2018, 08:20 AM
Replies: 1
Views: 611
Posted By blackgore
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...
Forum: Bioinformatics 09-04-2012, 06:32 AM
Replies: 7
Views: 4,372
Posted By blackgore
Hi Dan, thanks very much for the announcement,...

Hi Dan,
thanks very much for the announcement, and the new format seems to be working great!
Gordon
Forum: Bioinformatics 08-02-2012, 07:54 AM
Replies: 7
Views: 4,372
Posted By blackgore
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...
Forum: Bioinformatics 04-11-2012, 06:04 AM
Replies: 5
Views: 5,633
Posted By blackgore
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" ?
Forum: Bioinformatics 11-24-2011, 06:39 AM
Replies: 138
Views: 61,532
Posted By blackgore
The I/O exceptions are just slight warnings that...

The I/O exceptions are just slight warnings that the software can't "phone home" as it has to deal with proxies and firewalls and the like. It doesn't affect the result, and you can silence the...
Forum: Bioinformatics 11-24-2011, 06:17 AM
Replies: 138
Views: 61,532
Posted By blackgore
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...
Forum: Bioinformatics 05-04-2011, 02:32 AM
Replies: 48
Views: 57,958
Posted By blackgore
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...
Forum: Bioinformatics 05-03-2011, 11:54 AM
Replies: 48
Views: 57,958
Posted By blackgore
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,...
Forum: De novo discovery 11-17-2010, 07:29 AM
Replies: 58
Views: 40,880
Posted By blackgore
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...
Forum: Bioinformatics 06-28-2010, 06:08 AM
Replies: 46
Views: 25,905
Posted By blackgore
sorry Simon, I had meant to reply much sooner...

sorry Simon, I had meant to reply much sooner than this - thanks for your response, it was altogether very useful! :)
Forum: Bioinformatics 06-28-2010, 04:36 AM
Replies: 12
Views: 6,022
Posted By blackgore
I don't have a solution, but I do have the same...

I don't have a solution, but I do have the same problem..though not always.

I used tophat and cufflinks with no problems on a total of 7 different samples. running cuffdiff on two particular...
Forum: Bioinformatics 05-18-2010, 01:44 AM
Replies: 15
Views: 9,507
Posted By blackgore
is mirTools available for download, so that we...

is mirTools available for download, so that we could analyse data locally, add in our own reference genomes, etc?
Forum: De novo discovery 05-17-2010, 05:20 AM
Replies: 82
Views: 44,354
Posted By blackgore
How are people evaluating their transcriptome...

How are people evaluating their transcriptome assemblies? The standard N50 assessment can't be that useful, as the goal here isn't exactly to generate a tiny set of huge contigs...?
Forum: Bioinformatics 05-14-2010, 03:08 AM
Replies: 8
Views: 3,261
Posted By blackgore
it also wasn't the focus of my project at the...

it also wasn't the focus of my project at the time, so I didn't worry about it too much, I'm afraid.
Forum: RNA Sequencing 05-13-2010, 08:52 AM
Replies: 11
Views: 5,067
Posted By blackgore
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 -...
Forum: Bioinformatics 05-13-2010, 08:28 AM
Replies: 8
Views: 3,261
Posted By blackgore
I had a similar problem recently, and had to try...

I had a similar problem recently, and had to try another program (DESeq) for dealing with groups - unfortunately cuffdiff didn't support the use of replicates. With luck that will change in a future...
Forum: Illumina/Solexa 05-13-2010, 03:06 AM
Replies: 5
Views: 4,519
Posted By blackgore
Not the same analysis, I know, but the way this...

Not the same analysis, I know, but the way this thread is phrased, I saw (hallucinated?) some similarity between exome mapping and the alignment stage of an rna-seq experiment. To that end, could...
Forum: Bioinformatics 05-04-2010, 08:50 AM
Replies: 46
Views: 25,905
Posted By blackgore
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...
Forum: RNA Sequencing 03-16-2010, 04:08 AM
Replies: 11
Views: 5,067
Posted By blackgore
I also have replicates for some RNA-Seq data that...

I also have replicates for some RNA-Seq data that I'd like to group together, for the purposes of a differential expression test. However, in the Cufflinks manual I've only been able to find...
Forum: Bioinformatics 03-04-2010, 07:28 AM
Replies: 47
Views: 26,266
Posted By blackgore
This may be a naive question, as I'm only about...

This may be a naive question, as I'm only about to get into using Cufflinks (Bowtie and Tophat seem great though), but I have not been able to find any documentation about differential expression...
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