Forum: Bioinformatics
11-03-2014, 07:22 AM
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Replies: 2
Views: 847
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...
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Forum: Bioinformatics
09-26-2013, 12:41 PM
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Replies: 3
Views: 4,206
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...
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Forum: Bioinformatics
09-26-2013, 09:08 AM
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Replies: 3
Views: 1,423
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Forum: Bioinformatics
09-26-2013, 06:58 AM
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Replies: 3
Views: 1,423
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...
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Forum: Bioinformatics
06-22-2013, 01:35 PM
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Replies: 4
Views: 1,359
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Forum: Bioinformatics
06-22-2013, 01:34 PM
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Replies: 4
Views: 1,359
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.
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Forum: Bioinformatics
06-22-2013, 04:32 AM
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Replies: 4
Views: 1,359
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...
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Forum: General
01-25-2013, 02:31 PM
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Replies: 1
Views: 1,528
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. ...
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Forum: Introductions
10-27-2012, 08:38 AM
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Replies: 2
Views: 1,021
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Forum: Introductions
10-26-2012, 12:03 PM
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Replies: 2
Views: 1,021
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...
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Forum: Bioinformatics
05-06-2012, 05:14 PM
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Replies: 2
Views: 2,181
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...
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Forum: Bioinformatics
03-02-2012, 07:30 AM
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Replies: 11
Views: 8,167
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. ...
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Forum: Bioinformatics
03-01-2012, 08:15 PM
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Replies: 2
Views: 2,056
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...
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Forum: Bioinformatics
01-13-2012, 07:19 AM
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Replies: 1
Views: 1,703
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...
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Forum: Bioinformatics
12-13-2011, 03:05 PM
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Replies: 1
Views: 1,481
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...
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Forum: Bioinformatics
12-12-2011, 05:49 PM
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Replies: 4
Views: 7,001
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...
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Forum: Bioinformatics
12-12-2011, 01:49 PM
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Replies: 4
Views: 7,001
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...
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Forum: Sample Prep / Library Generation
10-26-2011, 10:33 AM
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Replies: 3
Views: 15,756
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Forum: Sample Prep / Library Generation
10-26-2011, 09:23 AM
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Replies: 3
Views: 15,756
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...
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Forum: Bioinformatics
10-13-2011, 02:55 PM
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Replies: 0
Views: 2,122
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...
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Forum: General
08-30-2011, 08:16 AM
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Replies: 1
Views: 2,142
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Forum: Bioinformatics
06-10-2011, 05:00 AM
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Replies: 2
Views: 4,300
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.
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Forum: Bioinformatics
06-10-2011, 04:40 AM
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Replies: 2
Views: 4,300
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.
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Forum: General
05-23-2011, 06:45 PM
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Replies: 1
Views: 2,120
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...
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Forum: Bioinformatics
04-07-2011, 02:19 PM
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Replies: 3
Views: 1,928
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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