Question: Adjacency Files For Abyss-Explorer
1
gravatar for 2184687-1231-83-
9.4 years ago by
2184687-1231-83-5.0k wrote:

Hi,

Where can I find example input files for abyss-explorer? Is the format specified somewhere?

assembly visualization • 2.0k views
ADD COMMENTlink written 9.4 years ago by 2184687-1231-83-5.0k
2

Hi, if you want answers to this question you should provide more instant information on the topic. This will also make this question useful to others, which it now definitely is not. What is abyss/ abyss-explorer? (It's a rather novel transcriptome assembler) http://www.ncbi.nlm.nih.gov/pubmed/19834150

Did you ask the authors: ibirol@bcgsc.ca, abyss-users@bcgsc.ca , ask them first, what did they answer?

I looked at the pages, seems like both programs are very poorly documented at first glance. Ask the authors for additional documentation, maybe.

ADD REPLYlink written 9.4 years ago by Michael Dondrup46k
3
gravatar for Rob Syme
9.4 years ago by
Rob Syme540
Perth, Western Australia
Rob Syme540 wrote:

On the ABySS-Explorer project page, there are links to two example data sets, a Human BAC clone assembly and an E.coli genome assembly.

The files that you need from your assembly are the adjacency file (.adj), the contigs (.fasta) and the distance file (.dist).

These files need to be in the same directory, and it's easiest to simply open them where they lie in the assembly folder.

ADD COMMENTlink written 9.4 years ago by Rob Syme540
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1713 users visited in the last hour