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Forum: Bioinformatics 08-06-2013, 08:25 AM
Replies: 0
Views: 1,722
Posted By rjohnp
PLINK association covariants issue

Hi all,

I am trying to do a GWAS in PLINK.

I am running

which give me an acceptable output with a subset of my desired covariants. However, I need to have both age and age^2 of the...
Forum: Bioinformatics 07-24-2013, 07:31 AM
Replies: 2
Views: 2,066
Posted By rjohnp
My understanding of the BAQ computation is that...

My understanding of the BAQ computation is that it alters the BAQ, particularly around indels, to my knowledge this would not benefit what I'm trying to do here?
Forum: Bioinformatics 07-10-2013, 06:16 AM
Replies: 2
Views: 2,066
Posted By rjohnp
Samtools mpileup calling independantly on multiple files

Hi all,

this may seem a rather odd question, I am ultimately looking to get a VCF file containing calls for all my samples in a batch of exomes.

The issue is, I want to have active reference...
Forum: Bioinformatics 04-08-2013, 01:15 AM
Replies: 11
Views: 3,446
Posted By rjohnp
When I get that sort of message it's generally a...

When I get that sort of message it's generally a trailing new-line on your input file. You should still have an output? Do a line count on your vcf file, I would suggest it's likely to be 120414...
Forum: General 04-05-2013, 08:08 AM
Replies: 7
Views: 1,667
Posted By rjohnp
Don't you just love technology, wANNOVAR gives...

Don't you just love technology, wANNOVAR gives you SIFT scores anyway I believe, plus all the rest, so the better out of the two to have working at least.

Amazing how the hardest part of...
Forum: General 04-05-2013, 06:08 AM
Replies: 7
Views: 1,667
Posted By rjohnp
I just tried: and that seemed to work...

I just tried:


and that seemed to work fine, if you're using this format, make sure to select 'ANNOVAR input format' for the input format.

If this does still not work...
Forum: General 04-05-2013, 04:32 AM
Replies: 7
Views: 1,667
Posted By rjohnp
http://www.openbioinformatics.org/annovar/annovar_...

http://www.openbioinformatics.org/annovar/annovar_input.html

As well as the positional (1 based) information, you also need to give it the reference and observed genotypes, tab delimited.

Chr ...
Forum: Bioinformatics 04-05-2013, 04:26 AM
Replies: 3
Views: 1,670
Posted By rjohnp
Hi, I've been doing a similar thing....

Hi,

I've been doing a similar thing. Depending on the format you have your SNPs in a custom Perl script worked a treat for me. I just concatenated them all into FASTA entries for each individual...
Forum: General 04-05-2013, 03:47 AM
Replies: 7
Views: 1,667
Posted By rjohnp
http://wannovar.usc.edu/ is a good server for...

http://wannovar.usc.edu/ is a good server for this. It will also annotate a plethora of other details such as the predicted damaging nature of non-synonymous changes (polyphen etc.) as well as minor...
Forum: Core Facilities 04-05-2013, 03:44 AM
Replies: 2
Views: 2,879
Posted By rjohnp
A valid point of course, but yes, we did check...

A valid point of course, but yes, we did check that all.

Very interesting actually, there are some good articles out there on lab automation, mainly for clinical path labs, some showing that...
Forum: Introductions 04-05-2013, 03:35 AM
Replies: 4
Views: 1,648
Posted By rjohnp
Hi, I know that feeling, I've gone straight...

Hi,

I know that feeling, I've gone straight from being a cellular biologist to doing my PhD in pure NGS data analysis, minimal Linux or coding experience prior.

It would help to know what...
Forum: General 04-04-2013, 02:03 PM
Replies: 15
Views: 27,966
Posted By rjohnp
Ts/Tv refers to the ratio between transitions and...

Ts/Tv refers to the ratio between transitions and transversions, the two classes of nucleotide chemical changes. Shown below (shamelessly nicked from...
Forum: Bioinformatics 04-04-2013, 01:27 PM
Replies: 11
Views: 3,446
Posted By rjohnp
Hi, VCF-tools has some useful tools for...

Hi,

VCF-tools has some useful tools for this sort of thing, see http://vcftools.sourceforge.net/perl_module.html#vcf-contrast. Looks like exactly what you're looking for.

Hope that helps.
Forum: Bioinformatics 04-04-2013, 08:47 AM
Replies: 3
Views: 1,443
Posted By rjohnp
Hi, the issue is that the 'score' must be...

Hi,

the issue is that the 'score' must be column 5, you have it in 4. From https://genome.ucsc.edu/FAQ/FAQformat.html:



If you just insert a 4th column with a name prior to the score column...
Forum: Sample Prep / Library Generation 04-04-2013, 08:16 AM
Replies: 0
Views: 1,445
Posted By rjohnp
Tolerances for non cells-of-interest for somatic variant calling

Hi,

we are looking at several types on non-solid tumors, so it is difficult to get a 'pure' sample of cancer cells for exome sequencing.

I was wondering what sort of level of purity of cancer...
Forum: Core Facilities 04-04-2013, 07:55 AM
Replies: 2
Views: 2,879
Posted By rjohnp
DNA Sample tracking

Hi all,

a not particularly intensive question here. We recently had a couple of sample identities mixed by our exome sequencing provider (i.e. we got back all our data but some of the .fastq...
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