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Search: Posts Made By: k-gun12
Forum: Illumina/Solexa 02-18-2018, 08:23 AM
Replies: 1
Views: 616
Posted By k-gun12
How many cycles from a 600-cycle kit?

Does anyone know how many cycles one can realistically push from a 600-cycle kit (does the SBS software even allow you to specify this any more?), and what happens when you run out of reagent? I am...
Forum: Bioinformatics 02-01-2018, 08:46 AM
Replies: 4
Views: 2,520
Posted By k-gun12
Thanks. I'll check those out. I don't mind...

Thanks. I'll check those out. I don't mind going commercial again, but the way Qiagen treated existing CLC customers as a cash cow after buying the company was pretty bad.
Forum: Bioinformatics 02-01-2018, 06:54 AM
Replies: 4
Views: 2,520
Posted By k-gun12
Alternative to CLC Genomics Workbench viewer

Qiagen has hiked the pricing and changed the licensing terms of the CLC software line to the point that I can no longer afford it after a decade of use. What I found myself using particularly in the...
Forum: Pacific Biosciences 11-18-2016, 08:30 AM
Replies: 8
Views: 3,321
Posted By k-gun12
I agree, but Illumina sequencing of these same...

I agree, but Illumina sequencing of these same cultures would not exhibit this problem. Granted, the assembly was in thousands and thousands of contigs, but there was no redundancy and the gene...
Forum: Pacific Biosciences 11-18-2016, 07:46 AM
Replies: 8
Views: 3,321
Posted By k-gun12
Thanks.. I have not yet tried Falcon. Maybe it's...

Thanks.. I have not yet tried Falcon. Maybe it's worth a shot. I think heterozygosity is a real problem for pacbio and I'm wondering if it is causing some of my issues. My samples are...
Forum: Pacific Biosciences 11-15-2016, 09:27 AM
Replies: 8
Views: 3,321
Posted By k-gun12
Systemic problem with PacBio data and chimeric contigs

I've got ~30x coverage of a small < 100MB algal genome using PB RSII. I corrected, assembled and polished the genome with Canu, and was pretty pleased with the results until I blasted the genome...
Forum: General 03-22-2015, 06:37 PM
Replies: 1
Views: 1,020
Posted By k-gun12
Motif enrichment

I have a degenerate motif, i.e AMNCDAYMNNTCA that I find clustered several times within 200bp of a 9kb contig. I need to test for enrichment there and qualify the likelihood of that happening (i.e...
Forum: General 11-16-2013, 11:35 AM
Replies: 0
Views: 3,341
Posted By k-gun12
A '3-taxon tree'

I've got transcriptomes from three closely related species A, B and their hybrid C. I'm trying to infer which genes from the hybrid have a closer affinity for A or B. I've seen some pubs do this by...
Forum: General 10-11-2013, 07:44 PM
Replies: 0
Views: 1,279
Posted By k-gun12
Finding purine/pyr rich motifs in genomes

This seems like a simple thing to find, but so far I've had no luck.. I need to scan some genome contigs for stretches of purine rich elements. Anyone have a nice tool to report this kind of thing?...
Forum: Bioinformatics 07-28-2013, 08:19 AM
Replies: 4
Views: 3,213
Posted By k-gun12
You won't be able to just align nucleotide...

You won't be able to just align nucleotide contigs and run the KaKs calculator.. it needs a codon alignment as input.. i.e properly aligned CDS sequence with no UTR and/or indels. A single indel...
Forum: Bioinformatics 03-14-2013, 09:50 AM
Replies: 0
Views: 987
Posted By k-gun12
Heuristic search for contaminant motifs

Is anyone aware of a tool to search DNA sequence data (i.e fasta) for repeated motifs that may be vector, adapter or other contaminant with no a-priori information? I'm thinking something like k-mer...
Forum: Bioinformatics 02-25-2013, 04:36 PM
Replies: 0
Views: 728
Posted By k-gun12
Pull CDS from EST assembly

Anyone have a favorite tool to pull a nucleotide CDS from an EST contig/assembly using a related proteome? I'm familiar with estwise, but it appears that 'estwise' is smart to frameshifts but won't...
Forum: Bioinformatics 12-29-2012, 04:10 PM
Replies: 1
Views: 888
Posted By k-gun12
Translate ESTs using related proteome

I've got denovo assembled RNAseq EST contigs from two subspecies of insect very closely related to one which has a nicely curated proteome. I want to compare protein sequences, but I need to first...
Forum: General 10-23-2012, 01:17 PM
Replies: 1
Views: 840
Posted By k-gun12
Phylogenetics question

This is a bit off-topic but it ties into NGS in that I've got de-novo whole-genome protein predictions from three organisms.. two ingroup and one outgroup taxa. I'm trying to figure out which...
Forum: Bioinformatics 03-21-2012, 05:03 PM
Replies: 6
Views: 3,507
Posted By k-gun12
I've got the same issue here... anyone found a...

I've got the same issue here... anyone found a solution yet?
Forum: Bioinformatics 03-12-2012, 06:14 PM
Replies: 0
Views: 704
Posted By k-gun12
searching for selection in two genomes

I've got a pretty curated genome sequence and a sister taxon I've de-novo assembled. I'd like to get a quick idea regarding what genes have been under selection since they diverged. Does anyone...
Forum: Bioinformatics 03-10-2012, 08:48 AM
Replies: 1
Views: 887
Posted By k-gun12
Finding circular DNAs

I've seen a few older threads on this, but no real consensus yet. Anyone have a script or method for finding circular DNAs (*osmids, minicircles) in an assembly? I suppose it's really just as...
Forum: Bioinformatics 12-15-2011, 08:55 AM
Replies: 1
Views: 1,167
Posted By k-gun12
Hyperthreading and BLAST

Does anyone have opinions as to the performance increase of blast on hyperthreaded Intel processors? We're trying to decide whether or not to assign slots to the hyperthreaded cores on our MPI...
Forum: General 08-12-2011, 11:38 AM
Replies: 0
Views: 880
Posted By k-gun12
Pulsed field electrophoresis of whole chromosomes

I'm looking for info regarding PFGE of eukaryotic chromosomes. I'd like to separate the three mosquito chromosomes and isolate the smallest of them for sequencing. Does anyone have info regarding...
Forum: Bioinformatics 05-27-2011, 09:33 AM
Replies: 2
Views: 1,321
Posted By k-gun12
Addendum: I see fasta2frag.tcl in mira does...

Addendum: I see fasta2frag.tcl in mira does this...
Forum: Bioinformatics 05-27-2011, 09:20 AM
Replies: 2
Views: 1,321
Posted By k-gun12
Fragment an assembly for later overlap

Can anyone recommend a tool to fragment an assembly into smaller overlapping reads or contigs? I have some assembled illumina data with larger contigs I want to break down into smaller <2kb contigs...
Forum: Bioinformatics 05-24-2011, 07:07 AM
Replies: 2
Views: 1,641
Posted By k-gun12
Thanks- I'll take a look. Basically I'm...

Thanks- I'll take a look. Basically I'm annotating a horizontal gene transfer into a eukaryote genome of a bacterial gene. It's now full of introns where it used to be in a single frame :(
Forum: Bioinformatics 05-23-2011, 01:10 PM
Replies: 2
Views: 1,641
Posted By k-gun12
Create protein translation from alignment?

I have a multiple alignment of a rather large protein. I also have a contig in my assembly that contains that protein, but there are many introns/frameshifts that make translating it difficult. Is...
Forum: RNA Sequencing 05-17-2011, 09:24 AM
Replies: 38
Views: 16,779
Posted By k-gun12
It turns out that a rather nice one is shipped...

It turns out that a rather nice one is shipped with EVidence Modeler:
http://evidencemodeler.sourceforge.net/

.. in the utilities directory.
Forum: General 03-19-2011, 07:48 AM
Replies: 0
Views: 1,567
Posted By k-gun12
FACS sorting chromosomes?

I've just read PNAS Yang et al. 2010, "Completely phased genome sequencing through chromosome sorting". Anyone else have experience sorting chromosomes on a FACS and have input on instrument...
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