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Forum: Bioinformatics 01-27-2015, 10:01 AM
Replies: 9
Views: 1,936
Posted By hiddenrisk
Hi- As I understand the documentation, you need...

Hi- As I understand the documentation, you need to have a sample data frame that has replicated information. As I read your sample table at present, you have 12 different levels for the conditions...
Forum: De novo discovery 10-18-2011, 08:08 AM
Replies: 4
Views: 1,890
Posted By hiddenrisk
Thank you for your help! I read the manual, and...

Thank you for your help! I read the manual, and also the wiki, and what I ended up doing was...

-short fasta short_fwd.fa short_rev.fa \
-shortpaired short_shuffled.fa \
-short...
Forum: De novo discovery 10-13-2011, 07:17 PM
Replies: 4
Views: 1,890
Posted By hiddenrisk
So, I managed to only sort of be successful... I...

So, I managed to only sort of be successful... I cannot include any singleton data when I run my assemblies.

Does anyone know how I might do this?
Forum: De novo discovery 10-13-2011, 07:39 AM
Replies: 4
Views: 1,890
Posted By hiddenrisk
So, I stumbled into the velvet page on the...

So, I stumbled into the velvet page on the seqwiki page and it answered my question, I think. I'll try doing what is suggested on the page, and let you all know how it works.
Forum: De novo discovery 10-13-2011, 07:21 AM
Replies: 8
Views: 10,808
Posted By hiddenrisk
Trinity questions...

Since we are talking about Trinity here, does anyone know the answers to the following questions:

1) What, explicitly is a "full-length transcript"? According to the second sentence of their...
Forum: De novo discovery 10-12-2011, 08:42 PM
Replies: 4
Views: 1,890
Posted By hiddenrisk
Velvet and reads from different generations of Illumina

Greetings colleagues!

I am a second year Ph.D. student and I am currently taking a genome assembly class. We have been given a class project to de novo assemble a set of reads. The data set...
Forum: Introductions 10-12-2011, 08:33 PM
Replies: 0
Views: 663
Posted By hiddenrisk
Greetings!

Hello everyone! I am a second year Ph.D. student at Texas A&M University. My dissertation (at this point) is going to involve transcriptome assembly of a non-model organism (a blow fly) that has...
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