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Search: Posts Made By: aaronh
Forum: Bioinformatics 11-03-2015, 05:26 PM
Replies: 2
Views: 1,875
Posted By aaronh
use #CHROM FROM TO WIDTH STRAND ...

use #CHROM FROM TO WIDTH STRAND FEATURE to mark it as a header line or just remove the line entirely.
Forum: Illumina/Solexa 10-07-2014, 09:10 AM
Replies: 9
Views: 1,586
Posted By aaronh
I ran into this issue with another data set. The...

I ran into this issue with another data set. The problem was SRA miss-parsed the fastq files. A few emails between the help desk and the original depositor resulted in SRA reformatting the files.
Forum: Sample Prep / Library Generation 08-15-2014, 02:02 PM
Replies: 1
Views: 1,667
Posted By aaronh
TruSeq PCR-Free odd peaks

We've used the TruSeq PCR-Free kit on very short fragments, 170bp, and are getting a double peak when looking at the results on the bioanalyzer (attached). Has anyone seen this before?
Forum: Bioinformatics 04-04-2014, 10:16 PM
Replies: 2
Views: 906
Posted By aaronh
These are the best motifs is my opinion. ...

These are the best motifs is my opinion. http://bergmanlab.smith.man.ac.uk/?page_id=274
I would scan for hits using paster or your favorite motif finder using 1-2kb around the tss.
Forum: Bioinformatics 11-26-2013, 06:12 PM
Replies: 3
Views: 1,575
Posted By aaronh
it look like you only ran it on chr22

it look like you only ran it on chr22
Forum: Illumina/Solexa 09-25-2013, 07:06 PM
Replies: 21
Views: 5,531
Posted By aaronh
Sounds like the first thing you need to do is...

Sounds like the first thing you need to do is work through something like http://ged.msu.edu/angus/ or http://intro-prog-bioinfo-2013.wikispaces.com/ Step 0 is to use Ubuntu or some kind of linux.
Forum: Bioinformatics 09-04-2013, 02:10 PM
Replies: 1
Views: 1,469
Posted By aaronh
MUMmer is a tool for whole genome alignments and...

MUMmer is a tool for whole genome alignments and it is not what you need. If you had two whole denovo assembled genomes then you would align them and look for differences. Since you already have...
Forum: Bioinformatics 08-26-2013, 11:52 AM
Replies: 6
Views: 1,164
Posted By aaronh
It is either flybase 5.something or dm3. They...

It is either flybase 5.something or dm3. They are the same thing, just with or without the leading chr.
Forum: Bioinformatics 08-26-2013, 11:08 AM
Replies: 6
Views: 1,164
Posted By aaronh
Here are the VCF files from the DGRP:...

Here are the VCF files from the DGRP: http://www.hgsc.bcm.tmc.edu/projects/dgrp/freeze2_Feb_2013/vcf_files/
Forum: Bioinformatics 06-21-2013, 01:14 PM
Replies: 1
Views: 923
Posted By aaronh
Split the genome into 128 intervals and run each...

Split the genome into 128 intervals and run each one separately, merging the VCF files after.
Forum: Bioinformatics 01-07-2013, 11:35 AM
Replies: 6
Views: 1,112
Posted By aaronh
Sure for a exploration of the data, it could be...

Sure for a exploration of the data, it could be useful. But most of the time, a raw view is not going to make your major point and it is still limited to a max number of segregating sites. The only...
Forum: Bioinformatics 01-07-2013, 10:28 AM
Replies: 6
Views: 1,112
Posted By aaronh
I like your image for small datasets but don't...

I like your image for small datasets but don't think it is very useful for large scale analysis. People did just show the segregating sites in old papers when they had only one gene to sequence....
Forum: Bioinformatics 12-27-2012, 09:56 AM
Replies: 10
Views: 3,520
Posted By aaronh
PloS One might be a great place for this.

PloS One might be a great place for this.
Forum: Bioinformatics 12-24-2012, 03:00 PM
Replies: 4
Views: 1,672
Posted By aaronh
Try using java -Djava.io.tmpdir=/path/to/tmpdir...

Try using java -Djava.io.tmpdir=/path/to/tmpdir -jar Add...
http://stackoverflow.com/questions/1924136/environment-variable-to-control-java-io-tmpdir
Some linux servers have a dedicated tmp...
Forum: Bioinformatics 12-24-2012, 02:37 PM
Replies: 4
Views: 1,672
Posted By aaronh
I've had issues when sorting if my tmp space...

I've had issues when sorting if my tmp space fills up. Did you try specifying the tmp dir?
Forum: Bioinformatics 12-18-2012, 03:16 PM
Replies: 7
Views: 1,490
Posted By aaronh
That number is also the max unsigned integer - 1...

That number is also the max unsigned integer - 1 so this smells like a Picard bug.
Forum: Bioinformatics 12-17-2012, 11:39 AM
Replies: 9
Views: 1,910
Posted By aaronh
At this point I think it is worth asking Gerton.

At this point I think it is worth asking Gerton.
Forum: Bioinformatics 12-13-2012, 11:29 AM
Replies: 9
Views: 1,910
Posted By aaronh
It could be a bad read. The samtools error means...

It could be a bad read. The samtools error means that the read and the corresponding quality score do not have the same length.

As for the sam output, try running it with a smaller test set like...
Forum: Bioinformatics 12-12-2012, 04:07 PM
Replies: 9
Views: 1,910
Posted By aaronh
Are you sure you should be using --solexa? I...

Are you sure you should be using --solexa? I could imagine wrongly calibrated quality scores inducing a ZeroDivisionError.
Forum: Illumina/Solexa 12-11-2012, 11:09 AM
Replies: 1
Views: 1,023
Posted By aaronh
I have no idea of dollar amount but I would try...

I have no idea of dollar amount but I would try to estimate how many reads you want. For example, how many reads were used to get good data in the ENCODE set? From there, you can look up the...
Forum: Bioinformatics 12-04-2012, 02:54 PM
Replies: 3
Views: 1,609
Posted By aaronh
samtools mpileup should give you what you need if...

samtools mpileup should give you what you need if you don't pass it to bcftools. Another way would be to load the bam file into IGV and get the summary there.
Forum: Bioinformatics 12-04-2012, 02:50 PM
Replies: 2
Views: 7,528
Posted By aaronh
I had a similar problem and the only way to fix...

I had a similar problem and the only way to fix it was to ask SRA to reformat it on their end. This required the input of the original submitter to verify how it should be split.
Forum: Bioinformatics 12-04-2012, 09:11 AM
Replies: 7
Views: 3,720
Posted By aaronh
Are you using the plain BWA or BWA-SW which is...

Are you using the plain BWA or BWA-SW which is designed for longer reads (>100bp)?
Forum: Bioinformatics 12-01-2012, 10:33 PM
Replies: 4
Views: 916
Posted By aaronh
One of the files it generates:...

One of the files it generates: SAMPLE_NAME.sample_summary has that. The sample_cumulative_coverage_proportions file will tell you how much of the genome is covered by some X.
Forum: Bioinformatics 12-01-2012, 09:44 PM
Replies: 4
Views: 916
Posted By aaronh
GATK's DepthOfCoverage will do this.

GATK's DepthOfCoverage will do this.
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