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Search: Posts Made By: Giles
Forum: Bioinformatics 11-03-2014, 07:22 AM
Replies: 2
Views: 793
Posted By Giles
groupBy to find max value

Does anyone know how i can use groupBy to find the max value, but print not the max value, but the position within the feature that the max value is associated with. To wit, if the value for a given...
Forum: Bioinformatics 09-26-2013, 12:41 PM
Replies: 3
Views: 4,176
Posted By Giles
BWA & multiple alignments per read

Bowtie clearly indicates in its manual that it will randomly assign any read for which there are multiple equally valid alignments. I can not see any such discussion regarding the "mem" aligner for...
Forum: Bioinformatics 09-26-2013, 09:08 AM
Replies: 3
Views: 1,366
Posted By Giles
with repeats, there is no way around bias. Its...

with repeats, there is no way around bias. Its just choosing which bias is the closest to the truth. anyway, how can you N-mask within bowtie?
Forum: Bioinformatics 09-26-2013, 06:58 AM
Replies: 3
Views: 1,366
Posted By Giles
masking specific regions during mapping

Is there a way to provide Bowtie2 (or BWA) with a file containing specific regions of the genome to ignore during mapping? I can't find such a command line argument in the manual, but I've missed...
Forum: Bioinformatics 06-22-2013, 01:35 PM
Replies: 4
Views: 1,307
Posted By Giles
Should I sort

Should I sort
Forum: Bioinformatics 06-22-2013, 01:34 PM
Replies: 4
Views: 1,307
Posted By Giles
Header looked fine. Size is ~3gb. Easily...

Header looked fine. Size is ~3gb. Easily converted into interval using galaxy. I've used this workflow dozens of times, this is the first occurrence of empty bam with no error.
Forum: Bioinformatics 06-22-2013, 04:32 AM
Replies: 4
Views: 1,307
Posted By Giles
problem with samtools view -bS

I've been using samtools view -bS on tons of datasets with no problems at all. My workflow is to fastq-dump a .sra file, then clip with fastx-clipper, then map with bowtie, then convert .sam to .bam...
Forum: General 01-25-2013, 02:31 PM
Replies: 1
Views: 1,494
Posted By Giles
qual format determination

I typically map fastq files taken from the short read archive using bowtie on Galaxy. I'm now moving to the command line. For this, I'll need to know what type of Qual format my fastq files are in. ...
Forum: Introductions 10-27-2012, 08:38 AM
Replies: 2
Views: 995
Posted By Giles
Yes. Just stumbled into that. Thanks.

Yes. Just stumbled into that. Thanks.
Forum: Introductions 10-26-2012, 12:03 PM
Replies: 2
Views: 995
Posted By Giles
integer to R,G,B

I'm toying w/ the various heatmap generation programs and find them all far too laborious for what I need. I have a series of locations, and a data value associated with each location. So thats 2...
Forum: Bioinformatics 05-06-2012, 05:14 PM
Replies: 2
Views: 2,120
Posted By Giles
grooming fastq dots to N's

I am trying to use various datasets from hudson alpha and the fastq files have dots in them. I don't know how to remove the dots. I'm not really a programmer, but I did try to remove them using...
Forum: Bioinformatics 03-02-2012, 07:30 AM
Replies: 11
Views: 8,019
Posted By Giles
sudden std bad alloc

I've been running bedtools on a virtual machine and have used genomeCoverageBed to make bedgraph files for months now. I didn't change anything, and all of a sudden the script throws std bad alloc. ...
Forum: Bioinformatics 03-01-2012, 08:15 PM
Replies: 2
Views: 2,012
Posted By Giles
std bad alloc

I have been running genomeCoverageBed from my command line for months now. it works fine. I have about 17GB of available RAM and plenty of hard drive space. All of a sudden, it started to throw...
Forum: Bioinformatics 01-13-2012, 07:19 AM
Replies: 1
Views: 1,667
Posted By Giles
CSHL Long RNA-seq dataset

I have uploaded the CSHL Long RNA-seq fastq dataset from the UCSC genome browser to galaxy and attempted to map the reads using bowtie, bwa and tophat. None of them are able to align more than a...
Forum: Bioinformatics 12-13-2011, 03:05 PM
Replies: 1
Views: 1,447
Posted By Giles
compiling BWA

I am running a virtualized fedora 15. I am no expert, but have successfully installed and been using BEDTools. I am now trying to install SAMTools and BWA. I am running into problems when I run...
Forum: Bioinformatics 12-12-2011, 05:49 PM
Replies: 4
Views: 6,930
Posted By Giles
The qual portion of fastq comes in different...

The qual portion of fastq comes in different varieties. Bwa and bowtie only accept one format. The galaxy fastq groomer changes the qual score format to allow bwa or bowtie compatibility. I would...
Forum: Bioinformatics 12-12-2011, 01:49 PM
Replies: 4
Views: 6,930
Posted By Giles
Fastq groomer from command line

Does anyone know of a script that allows one to convert Qual scores from a fastq file in order to map w/ BWA or Bowtie using the command line? I'm familar with the Galaxy tools function, but Galaxy...
Forum: Sample Prep / Library Generation 10-26-2011, 10:33 AM
Replies: 3
Views: 15,689
Posted By Giles
thanks for the info. That is exactly what I...

thanks for the info. That is exactly what I would have thought, but was hoping to get some confirmation.
Forum: Sample Prep / Library Generation 10-26-2011, 09:23 AM
Replies: 3
Views: 15,689
Posted By Giles
Multiplexing ChIP-seq

I am aware of two Illumina kits that can do multiplexing: the "multiplexing sample preparation oligonucleotide kit" and the "TruSeq sample preparation kit". The steps between these procedures and...
Forum: Bioinformatics 10-13-2011, 02:55 PM
Replies: 0
Views: 2,095
Posted By Giles
genomeCoverageBed

I'm getting "std bad::alloc" when I try to run genomeCoverageBed. I'm running it in Fedora virtualized w/ virtual box. It has 18GB of RAM. Even when I reduce the genome file to only a single...
Forum: General 08-30-2011, 08:16 AM
Replies: 1
Views: 2,098
Posted By Giles
Script for calculating the average distribution of tags per gene from ChIP-seq??

I seem to recall a script for calculating the average distribution of tags per gene from a ChIP-seq experiment. I thought this was a BEDTools script, but don't see it in there. I also couldn't find...
Forum: Bioinformatics 06-10-2011, 05:00 AM
Replies: 2
Views: 4,216
Posted By Giles
I think I got it

I went back to NCBI website and found a ncbi sra toolkit designed for 32 bit windows os. It seems to be working now.
Forum: Bioinformatics 06-10-2011, 04:40 AM
Replies: 2
Views: 4,216
Posted By Giles
Fastq-dump.exe

Has anybody gotten this to work using windows? If not, are there any ways to convert sra to fastq for someone on a windows OS? It seems that Galaxy has nothing regarding sra file formats.
Forum: General 05-23-2011, 06:45 PM
Replies: 1
Views: 2,085
Posted By Giles
Sample Prep Yields

I have recently gone through the generation of a ChIP-seq library using the standard Illumina protocol. According to this, I have done two gel purifications, one immediately following the adapter...
Forum: Bioinformatics 04-07-2011, 02:19 PM
Replies: 3
Gff
Views: 1,881
Posted By Giles
thanks...

but I am the same person that started that thread. I doubt the overlap between the two is 100% and figured it was quite small. All apologies for the redundancy.
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