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Forum: Illumina/Solexa 06-04-2012, 08:43 AM
Replies: 4
Views: 1,724
Posted By elgor
Thanks for your answers. I did exactly...

Thanks for your answers.



I did exactly that, but did get only a few reads with the searched TruSeq index sequence (and the undetermined reads of course). Not the expected 1/10 of all reads on...
Forum: Illumina/Solexa 06-04-2012, 12:56 AM
Replies: 4
Views: 1,724
Posted By elgor
How to find the "one" barcode?

Hi guys,

lets say we have 10 samples in a lane and only one of those samples has a barcode and I want to find the "one" sample which has this barcode, when I start the demultiplexing.

I know...
Forum: Illumina/Solexa 06-27-2011, 07:55 AM
Replies: 0
Views: 8,565
Posted By elgor
The position file formats ".clocs" and "_pos.txt"? Ist there any difference?

Is there any difference between the two position file formats ".clocs" and "_post.txt"? I suppose they contain the same information, because "bclToQseq accepts both as input, but why then is the...
Forum: Bioinformatics 06-16-2011, 08:40 AM
Replies: 3
Views: 2,600
Posted By elgor
Thanks a lot for the information (and the code!)...

Thanks a lot for the information (and the code!) fpepin and Brad-Chapman.

I suppose it is a bug, that "Basecalling_Netcopy_complete.txt" is created after the first read already and not...
Forum: Bioinformatics 06-14-2011, 07:49 AM
Replies: 3
Views: 2,600
Posted By elgor
In search of a sign in the data: When is a HiSeq run really done?

A maybe odd, but interesting question: Is there an easy way to see, if a HiSeq run has finished producing data, if you are not able to take a look at the HiSeq itself and its display? I mean, I would...
Forum: Bioinformatics 06-07-2011, 12:15 AM
Replies: 15
Views: 6,740
Posted By elgor
Sorry, I had forgotten about posting my solution...

Sorry, I had forgotten about posting my solution here. It solved a similar problem for a guy on the samtools/picard mailing list already:

[Samtools-help] Picard MarkDuplicates memory error on very...
Forum: Bioinformatics 05-26-2011, 12:56 AM
Replies: 15
Views: 6,740
Posted By elgor
It seems I've finally found a working set of...

It seems I've finally found a working set of arguments! After more than 14 hours it's still running! Fingers crossed, it keeps doing so and finishs successfully eventually.
Forum: Bioinformatics 05-25-2011, 08:45 AM
Replies: 15
Views: 6,740
Posted By elgor
Picard's MarkDuplicates -> OutOfMemoryError

Hi folks,

here comes my first question for you. I'm trying to remove duplicates from a big sorted merged BAM-file (~270 GB) with the help of Picard's MarkDuplicate function, but I'm running into...
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