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Forum: Bioinformatics 08-03-2018, 11:25 AM
Replies: 0
Views: 769
Posted By ewilbanks
Question Pilon ambiguous base handling?

Hi folks,

I'm using pilon to polishing a pacbio assembled genome with illumina data, and I'm confusing about how pilon treats single "N" characters for an ambigious base. There aren't gaps in the...
Forum: Bioinformatics 07-17-2014, 08:15 AM
Replies: 1
Views: 930
Posted By ewilbanks
blasr read length filter?

Hey folks,

I'm working with aligning some pacbio reads to a reference and have a question about blasr that I can't seem to figure out from the documentation. What I want is to only map the...
Forum: Bioinformatics 07-14-2014, 10:44 AM
Replies: 0
Views: 897
Posted By ewilbanks
crossmatch speed?

Hey folks,

Does anyone know if there are parameters that you can set when running cross_match within consed to speed things up? Its taking forever to search through my assembly with 9 contigs...
Forum: Bioinformatics 07-11-2014, 12:22 PM
Replies: 13
Views: 2,860
Posted By ewilbanks
Ah ha! Thank you!! I got lost in the massive...

Ah ha! Thank you!! I got lost in the massive manual pdf for the staden pacakge - found the documentation for doing what you describe on p. 28 Will try this now :) thanks again.
Forum: Bioinformatics 07-10-2014, 02:28 PM
Replies: 13
Views: 2,860
Posted By ewilbanks
Ah OK, thanks anyways! Yeah, I've looked into...

Ah OK, thanks anyways! Yeah, I've looked into these contig regions and see a drop in coverage, and no other competing overlaps with other contigs in the asm. Most are in regions w/ mobile genetic...
Forum: Bioinformatics 07-10-2014, 02:26 PM
Replies: 13
Views: 2,860
Posted By ewilbanks
Hey @JohnN, I've been looking into using...

Hey @JohnN,

I've been looking into using gap5 but can't figure out how to get it to accept / open my existing assembly. Do you have any pointers or suggestions? Links to other documentation? ...
Forum: Bioinformatics 07-08-2014, 08:58 AM
Replies: 13
Views: 2,860
Posted By ewilbanks
Fasta file of contigs I'm trying to merge is here...

Fasta file of contigs I'm trying to merge is here in case that's helpful...

https://dl.dropboxusercontent.com/u/2796343/unitig109_unitig111.fasta.gz
Forum: Bioinformatics 07-08-2014, 08:51 AM
Replies: 13
Views: 2,860
Posted By ewilbanks
Hey Brian, I tried testing dedupe.sh on two...

Hey Brian,

I tried testing dedupe.sh on two contigs that I checked out with nucmer first (see below). I've tried playing with the settings (overlap length, maxedits, etc...) but I can't seem to...
Forum: Bioinformatics 07-07-2014, 09:18 PM
Replies: 13
Views: 2,860
Posted By ewilbanks
Sweet, thanks! I'll give this a whirl tomorrow.

Sweet, thanks! I'll give this a whirl tomorrow.
Forum: Bioinformatics 07-07-2014, 12:49 PM
Replies: 13
Views: 2,860
Posted By ewilbanks
Merging contigs

Hi folks,

I'm parsing through the results of a pacbio assembly and have found places where two contigs could be merged into one - (>99%id, ~5k overlap) - but weren't by the assembler for whatever...
Forum: Bioinformatics 05-21-2014, 01:04 PM
Replies: 1
Views: 2,096
Posted By ewilbanks
Question MG-RAST KEGG mapper?

Hi folks,

I'm using MG-RAST to analyze my 454 metagenomic data and have run into an irritating feature - wondering if anyone has a workaround! In the KEGG map view, honing in on Nitrogen...
Forum: Bioinformatics 10-10-2013, 04:11 PM
Replies: 4
Views: 3,316
Posted By ewilbanks
Found a nice solution to this - in case anyone's...

Found a nice solution to this - in case anyone's ever looking...

http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64.v287/faSomeRecords
Forum: Bioinformatics 10-10-2013, 03:14 PM
Replies: 4
Views: 3,316
Posted By ewilbanks
Getting sequences from multiprotein .faa file?

Anyone have a favorite command-line method for grabbing specific entries from a FASTA Amino Acid (.faa) file? I have a list of sequences that I'd like to pull out of a larger file. I usually use...
Forum: Bioinformatics 09-30-2013, 02:31 PM
Replies: 0
Views: 849
Posted By ewilbanks
amos Bank2contig

Hi folks,

Wondering if anyone knows how to get a amos utilities to spit out a key showing the relationship between amos bank's IID for a read and that read's original name. I'm trying to get a...
Forum: Bioinformatics 09-27-2013, 02:44 PM
Replies: 1
Views: 3,076
Posted By ewilbanks
minimus2 assembly merge

Hi folks,

I'm using minimus2 to merge two different assemblies - a long read (LRseq - moleculo data) assembly done w/ celera and an idba_ud assembled illumina dataset. I've tried varying the...
Forum: Illumina/Solexa 06-04-2013, 11:30 AM
Replies: 11
Views: 5,640
Posted By ewilbanks
Does anyone happen to have a motif file for this...

Does anyone happen to have a motif file for this insertion site described in this reference above?
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3292447/

I'm trying to determine why there are...
Forum: Bioinformatics 05-10-2013, 03:45 PM
Replies: 0
Views: 870
Posted By ewilbanks
sam/bam to ace?

Does anyone know of a way to convert a sam or bam file to .ace ? Seems a bit odd but I have a specific program (Strainer (http://bioinformatics.org/strainer/wiki/) for viewing strain variants in...
Forum: Bioinformatics 05-10-2013, 03:42 PM
Replies: 4
Views: 2,203
Posted By ewilbanks
@empyrean Did you ever figure out how to do...

@empyrean

Did you ever figure out how to do this? I'm trying to do the same thing - trying to shove a bam file into an older program that expects either .ace or blastn.
Forum: Bioinformatics 05-10-2013, 03:38 PM
Replies: 27
Views: 11,890
Posted By ewilbanks
Hi folks - not sure if this has already been...

Hi folks - not sure if this has already been addressed, but there is a known issue with AMOS 3.1.0 release and celera assembler 7.0 release. As someone mentioned this is fixed in the development...
Forum: Bioinformatics 05-10-2013, 03:19 PM
Replies: 6
Views: 1,421
Posted By ewilbanks
where are you running hawkeye from? If you're...

where are you running hawkeye from? If you're running this from a machine that you have ssh'ed into - you need to login like this:

ssh -X username@yourserver.edu

Hawkeye is trying to launch...
Forum: Bioinformatics 05-03-2013, 09:24 AM
Replies: 17
Views: 3,251
Posted By ewilbanks
Great! I have noticed that too - for some reason,...

Great! I have noticed that too - for some reason, with these changes the minimum contig length cutoff doesn't seem to work properly. I've just been post-filtering to exclude the little stuff under...
Forum: Bioinformatics 05-02-2013, 09:01 AM
Replies: 17
Views: 3,251
Posted By ewilbanks
Nope - I just threw the two reads in directly...

Nope - I just threw the two reads in directly without end-assembling. Haven't tried assembling them together or anything yet.

To increase maxK, I modified src/basic/kmer.h and increased...
Forum: Bioinformatics 04-30-2013, 07:59 AM
Replies: 0
Views: 1,909
Posted By ewilbanks
idba_ud coassemble Miseq 2x250 and HiSeq 2x100 reads?

Hi folks,

I'm curious if anyone else has tried to use idba_ud co-assemble longer MiSeq data (2x250) with HiSeq data (2x100)? I've tweaked the source code to accept longer reads...
Forum: Bioinformatics 04-29-2013, 12:49 PM
Replies: 17
Views: 3,251
Posted By ewilbanks
my experience w/ assembling 2x250bp metagenomic...

my experience w/ assembling 2x250bp metagenomic data w/ idba_ud is that I saw little to no improvement using longer reads unless I increased the maxK to ~230-250. This will hog memory but assemblies...
Forum: Bioinformatics 04-10-2013, 05:26 PM
Replies: 5
Views: 7,541
Posted By ewilbanks
Are you folks wokring from idba-1.1.0 or 1.0.9? ...

Are you folks wokring from idba-1.1.0 or 1.0.9? I made the change above and it is altering only the max read length accepted, but not changing the maxK! When I try running it doesn't run saying my...
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