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Search: Posts Made By: Graham Etherington
Forum: Bioinformatics 10-18-2012, 02:18 AM
Replies: 2
Views: 2,390
Posted By Graham Etherington
Dan Koboldt has kindly given a full explanation...

Dan Koboldt has kindly given a full explanation of how the supplied p-value can affect genotype calls and genotype quality calculation at the VarScan Help forum at:...
Forum: Bioinformatics 10-17-2012, 12:02 AM
Replies: 2
Views: 2,390
Posted By Graham Etherington
VarScan mpileup2snp --p-value affects genotype call

Hi,
I'm using VarScan.v2.3.2 to analyse genotypes of susceptible and resistant plants. Sample1 is susceptible and Sample2 is resistant to a given pathogen.
I've noticed that when using mpileup2snp,...
Forum: Bioinformatics 09-25-2012, 02:43 AM
Replies: 4
Views: 1,966
Posted By Graham Etherington
Hi Adrian, I'm also new to VarScan. I wonder if...

Hi Adrian,
I'm also new to VarScan. I wonder if these figures are affected by the flag:
"--min-avg-qual Minimum base quality at a position to count a read [15]"
The Freq of 94.12% given in your...
Forum: Bioinformatics 04-03-2012, 06:16 AM
Replies: 3
Views: 3,002
Posted By Graham Etherington
How do I identify reads that overhang the end of a reference?

Hi,
I have 76nt single-end reads and I want to map them to a reference and identify the reads that overhang the end of the reference.
What would be the best mapper to do the mapping with?
If I use...
Forum: Bioinformatics 10-07-2011, 12:32 AM
Replies: 9
Views: 3,130
Posted By Graham Etherington
Thanks for your replies so far. To clarify, I'm...

Thanks for your replies so far.
To clarify, I'm only interested in just the library prep and chemical reagents cost of sequencing.
As to the point of sequence quality (i.e. Sanger being better...
Forum: Bioinformatics 10-06-2011, 12:35 AM
Replies: 9
Views: 3,130
Posted By Graham Etherington
The 'cost' of sequencing

Hi all,
I'm currently writing an article about sequencing and am trying make fair comparisons between the cost of sequencing 1Mb of DNA on the following machines:

ABI 3730xl (Sanger sequencing)...
Forum: Bioinformatics 10-04-2011, 07:17 AM
Replies: 3
Views: 3,307
Posted By Graham Etherington
Snappy comes distributed with the most recent...

Snappy comes distributed with the most recent versions of picard-tools (v1.53 - http://sourceforge.net/projects/picard/files/)
It's in the top-level directory by itself. The remaining picard jar...
Forum: Bioinformatics 09-08-2011, 12:56 AM
Replies: 10
Views: 6,401
Posted By Graham Etherington
There are a couple of things going on here....

There are a couple of things going on here. Firstly CollectInsertSizeMetrics thinks the BAM file isn't sorted, so you could try resorting it with samtools sort (and of course samtools index on the...
Forum: Bioinformatics 09-06-2011, 11:56 PM
Replies: 10
Views: 6,401
Posted By Graham Etherington
Yes. The gap size (or 'insert size' to give it...

Yes.
The gap size (or 'insert size' to give it the correct name) is included in the OUTPUT file of CollectInsertSizeMetrics. Amongst other statistical information, the following is given in relation...
Forum: Bioinformatics 09-03-2011, 03:03 AM
Replies: 10
Views: 6,401
Posted By Graham Etherington
You should use Picard for this: ...

You should use Picard for this:
http://picard.sourceforge.net/

The method 'CollectInsertSizeMetrics' reads a SAM or BAM file and writes a file containing metrics about the statistical...
Forum: Bioinformatics 09-02-2011, 05:40 AM
Replies: 10
Views: 6,401
Posted By Graham Etherington
Can you be a bit more specific. Which contigs...

Can you be a bit more specific.
Which contigs are you talking about - the reference? i.e. you want to use paired end sequences that map to different reference contigs to calculate the size of the...
Forum: Bioinformatics 07-20-2011, 04:45 AM
Replies: 2
Views: 5,805
Posted By Graham Etherington
Extract perfectly mapped reads from SAM/BAM file

Hi,
Given a SAM or BAM file, does anyone know how to identify which paired-sequences map perfectly to the reference? By perfectly mapped, I mean that the query is identical to the the reference (or...
Forum: Bioinformatics 03-21-2011, 03:51 AM
Replies: 13
Views: 10,076
Posted By Graham Etherington
The full results from the Assemblathon can be...

The full results from the Assemblathon can be found at:
http://assemblathon.org/
Forum: Bioinformatics 02-28-2011, 07:08 AM
Replies: 9
Views: 8,382
Posted By Graham Etherington
Would you care to share your solution so that...

Would you care to share your solution so that people searching for this problem have a possible answer.
Forum: Bioinformatics 01-06-2011, 01:49 AM
Replies: 10
Views: 8,306
Posted By Graham Etherington
Technically, what is 'insert-size'?

I've become slightly confused as to the use of the word 'insert-size' so I was wondering if someone could just confirm that my understanding of the term is correct.

If the fragment size excised...
Forum: Bioinformatics 10-18-2010, 03:58 AM
Replies: 1
Views: 8,884
Posted By Graham Etherington
Illumina 1.3 v 1.8 quality scores

Hi,
Is there/should there be any difference in the quality score format between Illumina 1.3 reads an Illumina 1.8 reads?
Many thanks,
Graham
Forum: Bioinformatics 05-18-2010, 07:58 AM
Replies: 5
Views: 7,930
Posted By Graham Etherington
Thanks. That should give me enough to get started...

Thanks. That should give me enough to get started with.
Best wishes,
Graham
Forum: Bioinformatics 05-18-2010, 01:52 AM
Replies: 12
Views: 45,114
Posted By Graham Etherington
Got it! Thanks (and sorry for being so thick ;))

Got it! Thanks (and sorry for being so thick ;))
Forum: Bioinformatics 05-18-2010, 12:26 AM
Replies: 12
Views: 45,114
Posted By Graham Etherington
A quick question about the Pileup format - if $...

A quick question about the Pileup format - if $ means a position where a read ends on the alignment, than can the example pileup given on the Samtools website ever be true?...
Forum: Bioinformatics 05-18-2010, 12:01 AM
Replies: 5
Views: 7,930
Posted By Graham Etherington
Hi, Thanks for your answer. I'd realised that...

Hi,
Thanks for your answer. I'd realised that Bio::DB:Sam couldn't parse the pileup, so this is why I am asking if anyone has, or knows about, anything that could parse it, before I spent time...
Forum: Bioinformatics 05-17-2010, 08:33 AM
Replies: 5
Views: 7,930
Posted By Graham Etherington
Samtools Pileup Parser

Hi,
I'm trying to parse the Samtools Pileup format in Perl.

I've created a paired-end assembly using BWA (aln, sampe) and then used Samtools to create a pileup (using import - sort - index -...
Forum: Bioinformatics 04-12-2010, 12:54 AM
Replies: 2
Views: 1,606
Posted By Graham Etherington
Hicham, This is not really the place you want...

Hicham,
This is not really the place you want to be asking this question, as this is a general programming question. If you decide what programming language you want to code in, then go to the...
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