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Forum: Bioinformatics 10-11-2014, 11:41 PM
Replies: 30
Views: 10,828
Posted By dnajuice
Unhappy DBI can't connect to local MySQL server (orthoMCL)

Dear friends,

I encountered similar situation (and this is the closest error message I could find), but could not work it out with the methods discussed here. I would appreciate very much if you...
Forum: Service Providers 10-03-2013, 11:24 AM
Replies: 8
Views: 3,661
Posted By dnajuice
Right - I am not looking for extremely rare...

Right - I am not looking for extremely rare events. In contrast, I am more interested in variants that exhibit high frequency on the PacBio. I have two questions here regarding PacBio: 1) Would ccs...
Forum: Service Providers 10-02-2013, 04:44 PM
Replies: 8
Views: 3,661
Posted By dnajuice
You are right. I need haplotypes and I must...

You are right. I need haplotypes and I must capture the 3 point mutations from each of the fragments. PacBio might work in this case due to the long read length, but I am concerned about the high...
Forum: Service Providers 10-02-2013, 01:36 PM
Replies: 8
Views: 3,661
Posted By dnajuice
targeted mutagenesis sequencing

I would like to sequence a pool (hundreds to thousands) of mutagenized variants, each with 3 point mutations at varying loci from the same parental sequence and the length of the sequence is ~1.5 kb,...
Forum: RNA Sequencing 11-08-2012, 10:52 AM
Replies: 1
Views: 1,702
Posted By dnajuice
Tools to study prokaryotic transcription start sites with RNA-Seq data

Hi,

Does anybody know any tools that can be utilized by bench scientists to identify/visualize transcription start sites (TSS) with RNA-Seq data generated for bacteria?

You opinion is much...
Forum: Bioinformatics 08-26-2012, 10:32 PM
Replies: 52
Views: 22,660
Posted By dnajuice
Hi Boetsie/Marten, I'm using SSPACE for...

Hi Boetsie/Marten,

I'm using SSPACE for contig extension and scaffolding, and it works pretty well. I am also interested in GapFiller. However, I'm a bit confused about the utility of contig...
Forum: Illumina/Solexa 08-25-2012, 02:17 PM
Replies: 0
Views: 2,227
Posted By dnajuice
export scaffold files from SAM/BAM alignment

Using BWA, I have aligned ~10M MiSeq paired end reads to ~100 sequence contigs obtained from non-paired end 454 data. Most of the contigs remained intact after aligning the paired end data, but some...
Forum: Bioinformatics 08-23-2012, 12:22 PM
Replies: 1
Views: 1,347
Posted By dnajuice
gsMapper failed to create ace or bam file

Hi,

I encountered a problem with gsMapper (v2.6) when I tried to align 10M Illumina paired end reads on to 100 large contigs. Even though I set the parameters to output file in ACE and BAM...
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