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Forum: Bioinformatics 04-29-2014, 05:19 PM
Replies: 8
Views: 3,846
Posted By Boonie
I am having trouble accessing asm2ace on...

I am having trouble accessing asm2ace on Sourceforge. Can you provide an active link?
Do you know of any other scripts that would convert a CA assembly to ace (or even bam)?
Thanks.
Forum: Pacific Biosciences 12-31-2012, 09:00 PM
Replies: 55
Views: 21,701
Posted By Boonie
LSC: beware the dinucleotide repeats

I am working with a ~1Gb genome and using 40X coverage of mer-trimmed Illumina reads. A test run on 100Mb of PacBio sequence took almost 10 days to complete on 40 cpus. As you know, LSC sorts the...
Forum: Sample Prep / Library Generation 04-08-2011, 07:19 AM
Replies: 3
Views: 13,498
Posted By Boonie
Nextera bias

If the DNA template is limited in quantity, could the bias in the Nextera output in some libraries be due to PCR amplification, even with only the recommended 9 cycles of amplification?
Forum: Illumina/Solexa 12-30-2010, 09:58 AM
Replies: 2
Views: 6,143
Posted By Boonie
Multiplex prep

We used the Nextera multiplex primers to prepare several bacterial libraries, then pooled the libraries for one lane of Illumina sequencing. This was quite straightforward following the...
Forum: De novo discovery 04-01-2010, 12:35 PM
Replies: 38
Views: 15,029
Posted By Boonie
A 454 - SSAHA approach

Just to throw in on the conversation, I pooled genomic DNA from 18 individuals, cut with a 4 base cutter, and sequenced a 15bp size fraction with two full runs of 454 reads (250bp). I assembled them...
Forum: De novo discovery 11-18-2009, 12:29 PM
Replies: 38
Views: 15,029
Posted By Boonie
Is there a need to obtain flanking sequence to...

Is there a need to obtain flanking sequence to design a genotyping assay? If so, how will you get sufficient flanking sequence if you are mapping short reads to the contig consensus seqs (assuming...
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