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Forum: Bioinformatics 04-01-2010, 04:26 PM
Replies: 0
Views: 1,672
Posted By agroster
consed newbie: how to export scaffold information

Hi, I recently ran a MIRA assembly of my 454 data and saved it to .ace file format. I can open it in consed with the -nophd function and consed will assemble the contigs using mate-pair data.
...
Forum: Bioinformatics 02-01-2010, 01:14 PM
Replies: 0
Views: 1,202
Posted By agroster
edena singletons

Does anyone know if it is possible to get the singletons (unused/unassembled sequences) from an EDENA assembly? Only three files are generated from the assembly, and none of these shows unused...
Forum: Bioinformatics 02-01-2010, 09:26 AM
Replies: 0
Views: 2,020
Posted By agroster
Illumina assemblies (w/ Edena) into Celera assembler

Hi,
I am doing de novo assembly with a lot of 454 and Illumina data that i have for my 7.3 Mb bacterial genome.

Data i have:
1.5 million 454 FLX and Titanium reads (average length ~320 bp)...
Forum: Bioinformatics 01-27-2010, 03:52 PM
Replies: 27
Views: 12,714
Posted By agroster
John, (jmarshall) - you are my saviour! I finally...

John, (jmarshall) - you are my saviour! I finally got it to install, after weeks of banging my head against the wall! The combination of adding the #include <cstdio> to four or five files and...
Forum: Bioinformatics 01-27-2010, 09:32 AM
Replies: 27
Views: 12,714
Posted By agroster
jmarshall, thanks for your reply. It was helpful...

jmarshall, thanks for your reply. It was helpful - I added the #include <cstdio> in the files that were giving me problems, and this got me through some errors. I indeed have the GCC compiler...
Forum: Bioinformatics 01-26-2010, 10:23 AM
Replies: 27
Views: 12,714
Posted By agroster
Thanks for the reply and thanks Arianda for the...

Thanks for the reply and thanks Arianda for the files. However, there was no change. I type $ ./configure, then "make", and still get the same errors:

IDMap_AMOS.cc: In member function ‘void...
Forum: Bioinformatics 01-26-2010, 06:30 AM
Replies: 27
Views: 12,714
Posted By agroster
Thanks for the reply, v_kisand. I've sent an...

Thanks for the reply, v_kisand. I've sent an email to Ariadna. I have been trying to install amos 2.0.8, not the short tools.

Looking forward to finally getting this resolved.
Forum: Bioinformatics 01-20-2010, 12:11 PM
Replies: 27
Views: 12,714
Posted By agroster
AMOS installation on 64-bit Linux

I keep banging my head against the keyboard trying to install the AMOS package on my 64-bit Linux system (Ubuntu 9.10). I think I have qt3 installed correctly, but I could be wrong.

If anyone has...
Forum: Bioinformatics 01-14-2010, 08:08 AM
Replies: 7
Views: 5,671
Posted By agroster
Ok, i now see the issue - I need to append my...

Ok, i now see the issue - I need to append my subsequent sff extractions using the "-a" option. i.e. do three subsequent extractions, each appending to the previous. I'll see if this works.
Forum: Bioinformatics 01-14-2010, 06:04 AM
Replies: 7
Views: 5,671
Posted By agroster
I concatenated the separate .fasta, .qual, and...

I concatenated the separate .fasta, .qual, and .xml files that were generated post sff_extract for each type of data, not the .sff files before sff_extract.

I DO want to give MIRA two separate...
Forum: Bioinformatics 01-13-2010, 09:51 AM
Replies: 7
Views: 5,671
Posted By agroster
Thanks for your reply. Since one set of my...

Thanks for your reply.

Since one set of my data is paired-end, i believe i need to force sff_extract to split up the reads by inducing the -l command to look for the linker. Also, mira requests an...
Forum: Bioinformatics 01-12-2010, 10:49 AM
Replies: 7
Views: 5,671
Posted By agroster
sff_extract: combining data from 454 Flx and Titanium data sets

Hi,
I am attempting to feed my 454 sequencing data sets into MIRA for assembly.
Here is my data, all in .sff files:
Flx unpaired reads (6 separate. sff files)
Titanium unpaired reads (3 separate...
Forum: Bioinformatics 01-06-2010, 04:08 PM
Replies: 3
Views: 2,820
Posted By agroster
celera assembler to .ace with multiple .frg files

Hi,
I have used Celera assembler to produce an assembly with three sets of data:
1. unpaired 454 FLX reads
2. unpaired 454 Tit reads
3. paired-end 454 Tit reads (10 Kb)

I used the sffToCA...
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