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Forum: Illumina/Solexa 10-29-2012, 01:53 PM
Replies: 2
Views: 5,131
Posted By NextGenSeb
Hi! Illumina published this Support Bulletin...

Hi!
Illumina published this Support Bulletin (https://my.illumina.com/myillumina/bulletin/hyLOtV_n-Ee6g1bH9ojDUg/considerations-for-library-migration-from-hiseq-ga) earlier this year titled...
Forum: Bioinformatics 05-13-2012, 09:02 PM
Replies: 43
Views: 11,682
Posted By NextGenSeb
Great, thanks again for your help. I'll give it a...

Great, thanks again for your help. I'll give it a go and let you know the outcome. Once I have results from the new chemistry I'' try to remember to put that up as well.

Cheers
Seb
Forum: Bioinformatics 05-13-2012, 07:35 PM
Replies: 43
Views: 11,682
Posted By NextGenSeb
Fair enough, maybe that gives me teh motivation...

Fair enough, maybe that gives me teh motivation to finally improve my almost non-existent python skills :)

Got a few more questions fo ryou though:

1. The "bed-like" format for candidate...
Forum: Bioinformatics 05-10-2012, 01:24 AM
Replies: 43
Views: 11,682
Posted By NextGenSeb
Hi Nils, just stumbled across dwgsim in my...

Hi Nils,
just stumbled across dwgsim in my search for a read simulator, love the fact that I can generate Illumina, Solid and Ion-torrent on the same tool as I have data from all platforms. Nice...
Forum: Ion Torrent 04-23-2012, 04:31 PM
Replies: 10
Views: 11,954
Posted By NextGenSeb
Hi all, have to agree with Stephen, the v2...

Hi all,

have to agree with Stephen, the v2 panel appears to be better than v1, both in coverage and workflow. But I do get those APC calls as well.

@ Stephen
Can you please elaborate on how...
Forum: Ion Torrent 04-02-2012, 03:59 PM
Replies: 10
Views: 11,954
Posted By NextGenSeb
Hi Sarah, I have had a couple of runs on the v1...

Hi Sarah,
I have had a couple of runs on the v1 ampliseq cancer panel, with mixed results re: amplicon coverage. Some appear to drop out systematically, however I understand that is a well known...
Forum: Epigenetics 03-05-2012, 12:11 PM
Replies: 5
Views: 3,145
Posted By NextGenSeb
Hi Unununium I agree with mark, you need to...

Hi Unununium

I agree with mark, you need to use a method that is better geared to identify differentially bound regions. I personally used MACS peak finder to identify regions of differential...
Forum: Bioinformatics 02-13-2012, 01:21 PM
Replies: 6
Views: 4,254
Posted By NextGenSeb
Hey Mary, I have traditionally used MACS...

Hey Mary,

I have traditionally used MACS peak finder to do the job, seemed to work well for well defined peaks like histone acetylation and H3K4me3, but struggled a bit with more extended peak...
Forum: Bioinformatics 02-13-2012, 01:12 PM
Replies: 6
Views: 4,698
Posted By NextGenSeb
Dear Wintec, in my opinion at this stage R...

Dear Wintec,

in my opinion at this stage R is the way to go, using packages like edgeR or DEseq. The time spend learning can be seen as a good investment in the future :)

However it really...
Forum: Bioinformatics 02-12-2012, 08:36 PM
Replies: 2
Views: 4,959
Posted By NextGenSeb
Very interesting blog, thanks for that!

Very interesting blog, thanks for that!
Forum: Illumina/Solexa 02-12-2012, 08:34 PM
Replies: 21
Views: 14,869
Posted By NextGenSeb
No, I don't have any script yet, and I think...

No, I don't have any script yet, and I think fastq is generally a good place to start. Also I think the handling of base-calling errors is important especially as the number of multiplexed samples...
Forum: Bioinformatics 02-08-2012, 03:28 PM
Replies: 2
Views: 4,959
Posted By NextGenSeb
GATK and Ion Torrent data

Hi all,

We have just started testing an Ion Torrent for variant detection in our lab, in order to compare it to other platforms. I am curious if anyone has tried using the PGM data in GATK? From...
Forum: Illumina/Solexa 02-08-2012, 03:14 PM
Replies: 21
Views: 14,869
Posted By NextGenSeb
Thanks for the replies guys :) @ECO: My...

Thanks for the replies guys :)

@ECO:
My Python is not brilliant, but I am happy to work on that. Would in general be interested in the LIMS integration anyway, as we use the same system and hope...
Forum: Illumina/Solexa 02-07-2012, 04:47 PM
Replies: 21
Views: 14,869
Posted By NextGenSeb
Hi ECO, would be great if you could provide...

Hi ECO,
would be great if you could provide the script you use to demultiplex the MiSeq FASTQ. We just got a MiSeq and I am not keen to use Illumina provided software for any of the analysis...
Forum: Ion Torrent 02-01-2012, 03:15 PM
Replies: 11
Views: 5,075
Posted By NextGenSeb
Hi Tucker303, recently looked into the same...

Hi Tucker303,

recently looked into the same question. In addition to the here stated concerns, the LifeScience rep made it quite clear that you waive your warranty if you install third party...
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