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Forum: Bioinformatics 08-04-2009, 06:21 PM
Replies: 13
Views: 15,581
Posted By Torst
From the manual: The split_on_index.py...

From the manual:

The split_on_index.py script identifies all read index sequences that are identical to the reference index sequences, or that differ by a user-defined number of bases. It then...
Forum: Bioinformatics 08-04-2009, 02:19 AM
Replies: 13
Views: 15,581
Posted By Torst
ohlsson, The nucleotide sequence instead of...

ohlsson,

The nucleotide sequence instead of the number must be new for GAPipeline 1.4. We are about to finish a multiplex run, so I will check what our files look like and let you know. But I...
Forum: Bioinformatics 04-16-2009, 05:05 PM
Replies: 13
Views: 15,581
Posted By Torst
Curt, I have fixed the 99/104 typo,...

Curt,



I have fixed the 99/104 typo, thank you for replying!

The 1.3 Pipeline user manual says it uses pure Phred scores -10*log10(e) but it does NOT clarify how it maps it to ASCII. As...
Forum: Bioinformatics 04-16-2009, 05:01 PM
Replies: 13
Views: 15,581
Posted By Torst
I am not 100% sure of the fields, and my...

I am not 100% sure of the fields, and my colleague has contacted Illumina for clarification, but what I do know I have added to the Wiki page:

http://en.wikipedia.org/wiki/FASTQ_format
...
Forum: Bioinformatics 04-15-2009, 07:49 PM
Replies: 13
Views: 15,581
Posted By Torst
Solution to Sanger/Solexa/Illumina FASTQ confusion

Many of the posts in this forum are with regard to confusion over the FASTQ format and the variations in quality value and ASCII encodings.

To help solve this once and for all, I have written a...
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