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Forum: Illumina/Solexa 10-07-2016, 05:33 AM
Replies: 0
Views: 3,078
Posted By Latrunculia
Primer filtering with bbduk / bbduk2.sh

Hello,

I have merged Illumina reads and try to filter out all reads that have both, a recognisable fwrd and a recognisable reverse primer and then to trimm those primers.

And I'd like to do...
Forum: Bioinformatics 06-30-2016, 10:41 PM
Replies: 0
Views: 1,717
Posted By Latrunculia
Using PyNAST as standalone program / PyNAST alternatives?

Hej

I am working on an Illumina paired-end Amplicon workflow. Now I need to align my unique reads in order to produce a phylogeny what in QIIME would be done with the align_seqs.py command,...
Forum: Illumina/Solexa 06-10-2016, 11:18 AM
Replies: 4
Views: 3,374
Posted By Latrunculia
Hey again. Thanks to both for your replies!...

Hey again.

Thanks to both for your replies! As Brian noted (and kindly told me by mail, too) the problem was the trailing tab. It works great now!

For the non-biological sequences, I found out...
Forum: Illumina/Solexa 06-10-2016, 01:39 AM
Replies: 4
Views: 3,374
Posted By Latrunculia
demultiplex FastQ files based on read names

Hi everybody,

my name is Fabian Roger and I am a PhD student in Ecology at the university of Gothenburg.

I am at a stage where I need to submit sequences to ENA but I don't have the files in...
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