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Forum: Bioinformatics 04-19-2016, 06:02 AM
Replies: 1
Views: 1,975
Posted By Alirez
Problem solved...

In case anyone is interested, when cap3 is called from a python script (using os.system) all the desired output files are produced. I haven't tested this yet, but it may well work for bash and perl...
Forum: Bioinformatics 04-18-2016, 03:54 PM
Replies: 1
Views: 1,975
Posted By Alirez
CAP3 not giving consensus and singlet files as output

Hi all,

I'm a bit confused as to why CAP3 is not giving .singlet and .contig output files as specified in the manual. The only output I am getting is the report of the assembly which I redirect...
Forum: Bioinformatics 11-23-2015, 08:46 AM
Replies: 2
Views: 1,296
Posted By Alirez
What is the best format for an external hard drive?

I've been having some trouble finding the right format for my external hard drive (Seagate Expansion Desktop Drive).

It will primarily be used in linux, but is a shared lab hard drive and is...
Forum: RNA Sequencing 10-23-2015, 08:42 AM
Replies: 5
Views: 1,405
Posted By Alirez
Brian and Westermen, Thanks for both of your...

Brian and Westermen,

Thanks for both of your comments, I'll use the bbmap as recommended.

With regards to the multiple-k approach I've been using it as a way to optimise my assembly - my...
Forum: RNA Sequencing 10-22-2015, 10:28 AM
Replies: 5
Views: 1,405
Posted By Alirez
Hi Brian, Thank you very much for your...

Hi Brian,

Thank you very much for your reply, I will look into doing this.

One further complication that I have is that I have generated a final assembly through a multiple k-mer approach. I've...
Forum: RNA Sequencing 10-22-2015, 09:14 AM
Replies: 5
Views: 1,405
Posted By Alirez
Acquiring reads not incorporated into a Trinity assembly?

Hi all,

I am conducting mRNASeq (Illumina HiSeq 2500 with PE data) using Trinity. I am finding it a bit difficult to see if there is an option to provide you with the reads which were not used to...
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