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Forum: Bioinformatics 11-29-2012, 06:10 PM
Replies: 13
Views: 4,454
Posted By AnthonyB
I've also been dealing with the problem of...

I've also been dealing with the problem of getting the scaffolds of SSPACE displayed in Hawkeye for assessment of assembly quality.

From my investigations, it seems that you have to parse the...
Forum: Bioinformatics 09-26-2011, 03:44 PM
Replies: 123
Views: 48,105
Posted By AnthonyB
Yes, I'm using maf2sam.py for the conversion and...

Yes, I'm using maf2sam.py for the conversion and I had noticed that there was currently no implicit paired-end distance set in the SAM file (Tablet reports all the lengths as 0). I'd be happy to...
Forum: Bioinformatics 09-25-2011, 10:21 PM
Replies: 123
Views: 48,105
Posted By AnthonyB
Hi, I have been experimenting with tablet to...

Hi,
I have been experimenting with tablet to view de novo assemblies produced with MIRA (via conversion from maf to bam). I was wondering if their was a way to set the paired-end coloring to...
Forum: Illumina/Solexa 10-29-2009, 06:45 PM
Replies: 3
Views: 2,569
Posted By AnthonyB
After skimming through the transcript of the...

After skimming through the transcript of the earning report, illumina say that the problem was with their paired-end kits which manifested itself as very high read errors in the 2nd read. It was...
Forum: Bioinformatics 08-11-2009, 05:22 PM
Replies: 24
Views: 16,424
Posted By AnthonyB
I think you can only obtain sffinfo as part of...

I think you can only obtain sffinfo as part of the sfftools package that is supplied by Roche to groups that have the 454 sequencing machines. I'm pretty sure that this was the basis behind the...
Forum: Bioinformatics 08-04-2009, 04:05 PM
Replies: 24
Views: 16,424
Posted By AnthonyB
Hi, AFAIK you only use the -s, -q or -x...

Hi,

AFAIK you only use the -s, -q or -x options if you want only one of the files. To get all three you only need to use the -o option to set the output name (if you want) and then the names of...
Forum: Bioinformatics 05-30-2009, 06:12 PM
Replies: 2
Views: 3,681
Posted By AnthonyB
I guess I should have been clearer in my post to...

I guess I should have been clearer in my post to say that the 150GB RAM requirement of SOAPdenovo for a human sized genome seems to be much lower than estimates I've seen for other short read de novo...
Forum: Bioinformatics 05-29-2009, 05:22 PM
Replies: 2
Views: 3,681
Posted By AnthonyB
SOAPdenovo

Has anyone tried the new SOAPdenovo program for assembling short reads and compared it to velvet etc? Their website claims that it can assemble human-sized genomes (eg panda) without crazy-high RAM...
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