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Forum: Bioinformatics 09-15-2017, 05:11 AM
Replies: 292
Views: 73,519
Posted By jazz710
The BBDuk commands don't have '-' before them....

The BBDuk commands don't have '-' before them. Your command should read:

bbduk.sh in=input.fq out=output.fq maxlength=10

Give that a shot?
Forum: Bioinformatics 08-12-2017, 12:29 AM
Replies: 211
Views: 50,671
Posted By jazz710
Re: reformat.sh Is there now, or could there...

Re: reformat.sh

Is there now, or could there be in the future, be a way to specify multiple sets of paired read inputs (ie. different libraries) which could be randomly sampled and output to a...
Forum: Bioinformatics 03-30-2016, 06:43 AM
Replies: 211
Views: 50,671
Posted By jazz710
Based on Brian's comments, I bet I have run out...

Based on Brian's comments, I bet I have run out of memory. My reference is very large, and a 3*K increase in memory would put me over my server capacity. I will try to re-run with a smaller reference.
Forum: Bioinformatics 03-30-2016, 06:37 AM
Replies: 211
Views: 50,671
Posted By jazz710
Based on a minute of observation, it appears to...

Based on a minute of observation, it appears to be sleeping, however the %CPU and %MEM change as I re-issue 'top'.
Forum: Bioinformatics 03-30-2016, 06:25 AM
Replies: 211
Views: 50,671
Posted By jazz710
http://www.public.iastate.edu/~literman/Screenshot...

http://www.public.iastate.edu/~literman/Screenshot%20from%202016-03-30%2009:20:50.png
Forum: Bioinformatics 03-30-2016, 06:11 AM
Replies: 211
Views: 50,671
Posted By jazz710
It was submitted to a server with a scheduler,...

It was submitted to a server with a scheduler, yes.

It's just odd that it's the exact same code and dataset, but the only difference is hdist=1...same set up with hdist=0 runs fine.
Forum: Bioinformatics 03-30-2016, 05:51 AM
Replies: 211
Views: 50,671
Posted By jazz710
There is no output yet... 40 threads, 800G...

There is no output yet...

40 threads, 800G memory.
Forum: Bioinformatics 03-30-2016, 05:32 AM
Replies: 211
Views: 50,671
Posted By jazz710
Thank you, as always for your thorough response!...

Thank you, as always for your thorough response! New question time:

I'm running a bbduk contamination removal and with normal settings, and the run takes ~30m-45m (it's a big dataset). However,...
Forum: Bioinformatics 03-24-2016, 07:38 AM
Replies: 211
Views: 50,671
Posted By jazz710
Cross Species Mapping

Hello Geno and Brian,

I have seen BBMap referenced on a handful of forums as a good option for mapping short DNA-seq reads onto a closely related species. Bowtie et al. can't seem to handle very...
Forum: Bioinformatics 03-18-2016, 06:34 AM
Replies: 211
Views: 50,671
Posted By jazz710
They were just basic kmercountexact.sh commands: ...

They were just basic kmercountexact.sh commands:

kmercountexact.sh -k <21-55> in=<File1> in2=<File2> mincount=2 prefilter=2

The graph included in my post above is the output from the Unique...
Forum: Bioinformatics 03-14-2016, 08:08 AM
Replies: 4
Views: 1,303
Posted By jazz710
For my data this is the header for my code: ...

For my data this is the header for my code:

# Load the libraries into R
library(spp)
library(Rsamtools)

# ONLY NEED THIS IF YOU WANT TO RUN ANALYSES ON MULTIPLE PROCESSORS (10 in this case)...
Forum: Bioinformatics 03-14-2016, 07:05 AM
Replies: 211
Views: 50,671
Posted By jazz710
Thanks GenoMax!

Thanks GenoMax!
Forum: Bioinformatics 03-14-2016, 06:49 AM
Replies: 211
Views: 50,671
Posted By jazz710
Kmer Counting

Hi Brian, tried to send you a private message, but I guess you're popular:

"Brian Bushnell has exceeded their stored private messages quota and cannot accept further messages until they clear some...
Forum: Bioinformatics 03-04-2016, 08:51 AM
Replies: 4
Views: 1,303
Posted By jazz710
I'll answer my own question. When I dove into the...

I'll answer my own question. When I dove into the source code a bit I found the following statement:

if (!is.element("fastcluster", installed.packages()[, 1])) {
stop("Rsamtools...
Forum: Bioinformatics 03-04-2016, 08:40 AM
Replies: 4
Views: 1,303
Posted By jazz710
SPP and Rsamtools Not Playing Nicely

Hello all,

I'm trying to analyze my ChIP-seq dataset using SPP but I keep getting the following error when I try to load my BAM files:

"Rsamtools Bioconductor package is now required for BAM...
Forum: Bioinformatics 01-22-2016, 06:58 AM
Replies: 0
Views: 980
Posted By jazz710
Odd Ray Error "Assembler panic: no k-mers found in reads."

Hi all,

I'm having an odd Ray error. I have a set of PE fastq files that are 35bp-101bp (confirmed through fastqc). When I run a Ray assembly with k=31, I get the following error:

Command:
...
Forum: Bioinformatics 12-10-2015, 05:25 AM
Replies: 278
Views: 95,595
Posted By jazz710
Can you explain Ray Surveyor in a bit more...

Can you explain Ray Surveyor in a bit more detail? I'm having a hard time understanding the documentation but I think this could be of use to me.
Forum: Bioinformatics 12-05-2015, 08:15 AM
Replies: 45
Views: 19,015
Posted By jazz710
Oh cool! Can I specify the kmer size? And can it...

Oh cool! Can I specify the kmer size? And can it accept paired end FASTQ files like the other tools? Ideally, I'd like to take a pair of PE FASTQs and extract the unique 31-mers (or some other value...
Forum: Bioinformatics 12-04-2015, 08:09 PM
Replies: 45
Views: 19,015
Posted By jazz710
Unique kmers from BBNorm?

Brian,

I see that in the output of BBNorm there are counts of unique kmers. Is there an option within BBNorm to export the unique kmers as a list or FASTA?

Best,

Bob
Forum: Bioinformatics 10-27-2015, 08:18 AM
Replies: 118
Views: 42,515
Posted By jazz710
How to use merged reads

Brian,

Cool tool (as always)! I'm loving the Geneious integration for these tools. A+ move on your part.

I'm performing my first merges on some raw and trimmed datasets and I had a very basic...
Forum: Bioinformatics 03-11-2015, 07:52 AM
Replies: 292
Views: 73,519
Posted By jazz710
I'd like to make a brief suggestion, thought it's...

I'd like to make a brief suggestion, thought it's obviously not important in the grand scheme.

I thought it would be nice if there was a batch setting for BBDuk. Currently, I have 48 fastq files...
Forum: Bioinformatics 01-29-2015, 10:04 AM
Replies: 45
Views: 19,015
Posted By jazz710
Hi Brian, I'm trying to do some...

Hi Brian,

I'm trying to do some normalization but I want to set my target coverage to 10X rather than 40X. Is there any way to change that in BBNorm? I tried target=10, but it still says 40X on...
Forum: Bioinformatics 01-29-2015, 08:49 AM
Replies: 9
Views: 1,863
Posted By jazz710
Yes, and I'm seeing now as well that one of the...

Yes, and I'm seeing now as well that one of the two isolates has a very high amount of duplication as well :-/

I'll take a look at the haploid assemblers!
Forum: Bioinformatics 01-29-2015, 08:38 AM
Replies: 9
Views: 1,863
Posted By jazz710
Slightly different system, this isn't chromosomal...

Slightly different system, this isn't chromosomal rearrangements. This is hybridization with whole new chromosome arms. :) The sequence differences should be large and in charge.
Forum: Bioinformatics 01-29-2015, 06:05 AM
Replies: 9
Views: 1,863
Posted By jazz710
That seems like a slice of fried gold right...

That seems like a slice of fried gold right there! I'll play around with it for sure.
Showing results 1 to 25 of 41

 


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