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Forum: De novo discovery 10-17-2013, 06:31 PM
Replies: 0
Views: 1,119
Posted By Andres_Gomez
Coverage peak values meta-velvetg

Hi

I have a metagenomic dataset composed by ~300 Million pair end reads (HiSeq) 150 bp read length and ~380 average fragment size.

I'm trying to run meta-velvet to assemble metagenomes. After...
Forum: De novo discovery 10-07-2013, 05:00 PM
Replies: 1
Views: 1,656
Posted By Andres_Gomez
velvetg ins_length parameter

Hi

I have a very simple question regarding the velvetg command, I really don't know what to provide in the ins_length parameter. My Reads were produced with a HiSeq instrument and are 150nt in...
Forum: Bioinformatics 09-30-2013, 02:52 PM
Replies: 0
Views: 1,116
Posted By Andres_Gomez
To Assemble or not to Assemble (Illumina short reads-microbial metagenomic data)

Hi all.
This may seem a more philosophical than procedural question, but I'm gonna give it a shot here any way.
I recently got a metagenomic dataset generated on a HiSeq2500 using a TruSeq kit for...
Forum: Bioinformatics 08-06-2013, 11:50 AM
Replies: 12
Views: 1,497
Posted By Andres_Gomez
Worked wonders! thanks a lot atcghelix, mastal,...

Worked wonders! thanks a lot atcghelix, mastal, kmcarr, SES and everybody else giving advice. :)
Forum: Bioinformatics 08-05-2013, 08:05 PM
Replies: 12
Views: 1,497
Posted By Andres_Gomez
Any clues on where I should change the names? is...

Any clues on where I should change the names? is it lines 11 and 19?
Forum: Bioinformatics 08-05-2013, 04:49 PM
Replies: 12
Views: 1,497
Posted By Andres_Gomez
I tried running the code you provided as: ...

I tried running the code you provided as:
Desktop $ perl merge.pl -code Howler.final.groups -seq Howler.final.fasta -output >merged.txt

and goy this error:

readline() on closed filehandle...
Forum: Bioinformatics 08-05-2013, 04:14 PM
Replies: 12
Views: 1,497
Posted By Andres_Gomez
Thanks, can you give me a hand in usage?

Thanks, can you give me a hand in usage?
Forum: Bioinformatics 08-05-2013, 03:18 PM
Replies: 12
Views: 1,497
Posted By Andres_Gomez
perl_merge fasta and group files (454)

Hi

I am trying to put data from 454 that I have de noised and compiled with mothur to start using qiime and PICRUSt. So I need to merge two files that look like this:

A fasta file:...
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