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Search: Posts Made By: cam.jack
Forum: Bioinformatics 08-01-2012, 05:58 PM
Replies: 4
Views: 2,569
Posted By cam.jack
The first paragraph you read is for end-to-end...

The first paragraph you read is for end-to-end alignment and the 2nd is for local alignment. They are different methods with different scoring systems.
Forum: Bioinformatics 08-01-2012, 05:43 PM
Replies: 5
Views: 1,537
Posted By cam.jack
I would have thought MAQ was totally outdated...

I would have thought MAQ was totally outdated now. Does it even output to SAM?

With Illumina 1.3+ to 1.7 you need to use the -I flag with BWA.
Forum: Academic/Non-Profit Jobs 07-17-2012, 09:50 PM
Replies: 4
Views: 1,460
Posted By cam.jack
Employ a Comp-Sci grad and help them pay their...

Employ a Comp-Sci grad and help them pay their rent. I also didn't realise this was the 'classifieds' section.
Forum: Bioinformatics 06-12-2012, 10:06 PM
Replies: 6
Views: 3,238
Posted By cam.jack
The XT:A:R flag is generated by a different...

The XT:A:R flag is generated by a different alogrithm to the MAPQ score - so they can have different answers!

The question is which algorithm do you believe? BW alignment creates the XT flag - so...
Forum: Bioinformatics 06-12-2012, 05:19 PM
Replies: 6
Views: 3,238
Posted By cam.jack
Hi Morangal, I suspect that in these cases...

Hi Morangal,

I suspect that in these cases the reads can also be mapped correctly to a second location. MAPQ = 0 if reads map perfectly in two places. This should be possible for short reads and...
Forum: Bioinformatics 03-29-2012, 08:31 PM
Replies: 6
Views: 3,238
Posted By cam.jack
They are produced by different algorithms. Mapq...

They are produced by different algorithms. Mapq is produced by Smith-Waterman Alignment while the XT flags come from Burrows-Wheeler Transform search.

What I want to know, is which (if either) do...
Forum: Bioinformatics 11-03-2011, 05:39 PM
Replies: 10
Views: 2,909
Posted By cam.jack
Thanks for that Ori, :)

Thanks for that Ori, :)
Forum: Bioinformatics 11-01-2011, 04:08 PM
Replies: 10
Views: 2,909
Posted By cam.jack
Ori - it would be very helpful if you said how...

Ori - it would be very helpful if you said how big you expected your final genome to be and the expected coverage you have (also the length of your reads would be good).

Thanks.
Forum: Bioinformatics 06-14-2011, 07:06 PM
Replies: 7
Views: 7,268
Posted By cam.jack
Very strange but it seems that it was the piping...

Very strange but it seems that it was the piping from one process to another that broke it!

I've now taken every process call and separated it out on to its own line and now it works.

Thanks...
Forum: Bioinformatics 06-13-2011, 06:50 PM
Replies: 7
Views: 7,268
Posted By cam.jack
Can't see how to private message you sorry. Here...

Can't see how to private message you sorry. Here is a section my VCF for chromosome 4. I'll give your suggestion a crack now. Would still love know what's going on. The manuals only ever hint at what...
Forum: Bioinformatics 06-12-2011, 10:54 PM
Replies: 7
Views: 7,268
Posted By cam.jack
Unhappy Mpileup/BCFtools pipeline not picking up indels (suggestions please)

Hi Everyone. I've googled long and hard for this, as well as trying every parameter that I can think of, but my indel detection pipeline is only picking up SNPs.

I know this because I introduced...
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