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Search: Posts Made By: Oyster_lab
Forum: Bioinformatics 07-16-2015, 08:41 PM
Replies: 1
Views: 1,689
Posted By Oyster_lab
Hi Jack, I'm having the same issue and would...

Hi Jack,

I'm having the same issue and would like to hear some suggestions on how to move further. I have ~40% of Blast hits, many of them with predicted/hypothetical proteins.

How did you...
Forum: De novo discovery 11-18-2014, 03:58 AM
Replies: 3
Views: 3,390
Posted By Oyster_lab
Hi all, I'm facing a similar error at the...

Hi all,

I'm facing a similar error at the moment., but for Oases. I've downloaded and compiled Velvet (version 1.2.09) using " $make " and also " $make 'MAXKMERLENGTH=64' ". Following that, I've...
Forum: Bioinformatics 10-26-2014, 06:25 PM
Replies: 11
Views: 9,009
Posted By Oyster_lab
Post And what about combining PE reads from multiple...

And what about combining PE reads from multiple runs? I have two runs from the same library and I would like to combine the PE reads into the same file (one file for R1 and one file for R2), keeping...
Forum: RNA Sequencing 06-30-2014, 01:37 AM
Replies: 1
Views: 1,791
Posted By Oyster_lab
Combining de novo assembly and reference scaffold

What is the best way to combine de novo and reference-guided assemblies? The scaffold of a closely-related species is available and I would like to use it to improve the de novo assembly I have done....
Forum: RNA Sequencing 06-24-2014, 07:47 PM
Replies: 23
Views: 73,543
Posted By Oyster_lab
Thanks for your reply, Brian. I have mRNA...

Thanks for your reply, Brian.
I have mRNA Illumina 100bp paired end reads. I have already removed the adapters, but still have that same the high variation on GC% at the 5' end. For the library...
Forum: RNA Sequencing 06-24-2014, 07:23 PM
Replies: 23
Views: 73,543
Posted By Oyster_lab
So, just following up on this topic. It has been...

So, just following up on this topic. It has been incredibly helpful. We shouldn't trim the first bases at the 5' end and try to perform the de novo assembly that way correct?

Thanks!
Forum: Bioinformatics 06-24-2014, 07:09 PM
Replies: 3
Views: 3,827
Posted By Oyster_lab
Hi! Following up on this question, should I...

Hi!
Following up on this question, should I remove adapters from both strands?
I am using CLC for read trimming, and have paired end 100 bp Illumina reads.
Forum: Sample Prep / Library Generation 04-09-2014, 03:45 PM
Replies: 26
Views: 33,882
Posted By Oyster_lab
Hi, It was relieving to find this forum. I...

Hi,

It was relieving to find this forum. I just had my samples ran on Bioloanalizer and they look exactly as you have described (and how it is in the article posted): group of small peaks until...
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