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Old 04-04-2011, 02:13 AM   #21
Location: Europe

Join Date: Mar 2011
Posts: 14

That is weird!!! the last time I tried it din't work and now it is reading the file! I'll cross my fingers and hope for the best. Do you have any idea how long it could take? I read somewhere that it can take between 3 and 10 hours...
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Old 04-04-2011, 02:31 AM   #22
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Location: Marburg, Germany

Join Date: Oct 2009
Posts: 110

that depends.
What exactly are you trying to assemble, how many reads do you have, etc?.

Generally, assembly can take a long (long) time.
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Old 06-09-2011, 07:29 AM   #23
Junior Member
Location: Poland and Germany

Join Date: Jun 2011
Posts: 1

Hi all, I'm new here and have a problem.
Maybe its not right place to write but I can not write new post.

I'm using the ABySS for 36bp sequences and now will use the trans-ABySS.

I used command: for k in {18..35}; do ABYSS <file to analyze> -o <where save the file>-k@$k.fa;

My input was file with contigs (after format: fastanrdb) with FASTA extenstion.

I got from ABYSS analysis files. They looks like (examples):

>0 31 117
>1 35 79
>2 27 60
>3 44 666
>4 111 1332
>5 18 31
>6 38 213

I have problem with next step of analysis-the trans-Abyss

In manual guide I read that the trans abyss needs specific folder structure.

I dont know what does it means, because I put my results from abyss (in fasta) in folders: LIB0001/kn(15-35)/...fasta (from abyss)

I dont know what is next?

sorry for so complicates question but I am so sad sitting, reading and nothing.....
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