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Search: Posts Made By: bw.
Forum: Bioinformatics 02-12-2014, 09:55 PM
Replies: 10
Views: 4,026
Posted By bw.
@swbarnes2 cool. never realized there was a...

@swbarnes2 cool. never realized there was a difference.

@oyvindbusk thanks, I also tried this and ended up with similar thresholds (male < 40% and female > 50%). I didn't try to filter out...
Forum: Bioinformatics 02-04-2014, 03:26 PM
Replies: 22
Views: 10,113
Posted By bw.
I'm also seeing the slashes with VarScan v2.3.6 ...

I'm also seeing the slashes with VarScan v2.3.6
I wrote this script to convert the slashes to commas:


import sys

if len(sys.argv) < 2: sys.exit("Usage: " + sys.argv[0] + " vcf_filename")
...
Forum: Bioinformatics 12-07-2013, 10:12 PM
Replies: 11
Views: 7,873
Posted By bw.
I recently ran into the same error: Couldn't...

I recently ran into the same error:

Couldn't build bowtie index with err = 1

I ran bowtie2-inspect -n but the name exactly matched the name in the 1st column of the GTF. I then ran ...
Forum: Bioinformatics 12-04-2013, 02:39 AM
Replies: 10
Views: 4,026
Posted By bw.
Testing sex determination with CCLE samples

I've tried using [num reads mapped to chrX] / [num reads mapped to chrY]
to determine sex in some CCLE exome-seq samples. The ratios turned out to be:



So it looks like the difference is...
Forum: Bioinformatics 11-12-2013, 10:22 PM
Replies: 149
Views: 43,921
Posted By bw.
Thank you Wei. I switched to using featureCounts....

Thank you Wei. I switched to using featureCounts.
Its especially great that it now takes multiple .bam files.

Whatever statistics can be provided in future versions will be helpful.
Forum: Bioinformatics 11-05-2013, 05:11 AM
Replies: 3
Views: 1,134
Posted By bw.
Thanks gringer - I took a look at that Galaxy...

Thanks gringer - I took a look at that Galaxy instance, but didn't see much in the way of QC (other than FastQC).
Forum: Bioinformatics 11-05-2013, 02:11 AM
Replies: 2
Views: 981
Posted By bw.
Also curious about this. Perhaps they are using...

Also curious about this. Perhaps they are using pooled normals?
If library prep & sequencer are the same, and the pooled samples are copy-number neutral, it should be possible to get decent results...
Forum: Bioinformatics 11-05-2013, 02:06 AM
Replies: 2
Views: 2,442
Posted By bw.
-n mode only considers mismatches in part of the...

-n mode only considers mismatches in part of the read sequence (in the seed). Also, it takes the base quality scores into account when deciding what is the best alignment.
(See point 2. here...
Forum: Bioinformatics 11-05-2013, 12:26 AM
Replies: 2
Views: 1,109
Posted By bw.
You can use the GATK VariantAnnotator...

You can use the GATK VariantAnnotator (http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_annotator_VariantAnnotator.html) .

So something like:

java -jar...
Forum: Bioinformatics 11-04-2013, 11:39 PM
Replies: 3
Views: 1,134
Posted By bw.
QC'ing NGS data

Hi all,
What tools are people using for QC'ing the initial stages of NGS data analysis?

I'm thinking tools that run on
- unaligned .fastq
- aligned .bam
- single vs. paired end
-...
Forum: Bioinformatics 11-04-2013, 10:54 PM
Replies: 0
Views: 1,269
Posted By bw.
[deleted this post]

[deleted this post]
Forum: Bioinformatics 11-04-2013, 09:20 PM
Replies: 149
Views: 43,921
Posted By bw.
Hi, I would like to use featureCounts, but...

Hi,
I would like to use featureCounts, but miss the stats provided by htseq-count (copied below) as these let me make sure I got the 'strand' setting right and other things.
Any chance you could...
Forum: Bioinformatics 10-29-2013, 11:24 AM
Replies: 35
Views: 11,003
Posted By bw.
Downsampling giving strange results

I ran a comparison to get a feel for Preseq and picard estimates using 5 real exome seq samples (50bp paired-end) with 50 million reads each. For each of the samples, I downsampled to between 10% and...
Forum: Bioinformatics 07-08-2013, 08:46 AM
Replies: 3
Views: 5,334
Posted By bw.
In this case the issue is probably the "BAM?"...

In this case the issue is probably the
"BAM?" on the 1st line in front of "@HD VN:1.0 GO:none SO:unsorted"
I would try deleting it.
Forum: Bioinformatics 06-24-2012, 10:03 PM
Replies: 1
Views: 2,416
Posted By bw.
merging fastq running bwa gives different results from running bwa then merging sam.

I have an exome seq dataset with 2x100bp paired end reads.
CASAVA 1.8 generated multiple .fastq files for each pair:

L002_R1_001.fastq.gz
L002_R1_002.fastq.gz
L002_R1_003.fastq.gz
...
Forum: Literature Watch 05-18-2012, 03:37 PM
Replies: 9
Views: 5,454
Posted By bw.
I'm running CREST on exome seq samples. On 8...

I'm running CREST on exome seq samples.
On 8 out of the approx. 50 samples, the tool hangs after partially running through the step where it prints:

Output is in...
Forum: Literature Watch 05-18-2012, 03:05 PM
Replies: 76
Views: 29,336
Posted By bw.
That would really useful! My backup was to use...

That would really useful!
My backup was to use per-exon mean target coverage generated by Picard HS Metrics, with some added correction for %GC, but I'd rather use your tool.
Thanks,
-Ben
Forum: Literature Watch 05-18-2012, 12:52 PM
Replies: 76
Views: 29,336
Posted By bw.
Calling CNA and BAF for exome seq data without a control

Hi, I'm trying to use FREEC to call CNA and BAF in some exome seq samples, but haven't been able to make it work. The tool ran fine on the chr19 test data.

The problems I'm seeing are
- the tool...
Forum: Bioinformatics 05-18-2012, 12:28 AM
Replies: 12
Views: 5,966
Posted By bw.
Also getting this error with samtools 0.1.17 and 0.1.18

Hi,
I'm running samtools on a 64bit linux server after compiling the tool on this server using make (no issues during the compilation).

I'm getting the float point error and it happens even if...
Forum: General 04-08-2012, 11:50 PM
Replies: 23
Views: 107,312
Posted By bw.
Great intro for a relatively new user. Thanks.

Great intro for a relatively new user. Thanks.
Forum: Bioinformatics 04-08-2012, 11:41 PM
Replies: 2
Views: 3,847
Posted By bw.
I also had this question earlier. This post...

I also had this question earlier. This post cleared some things up:

http://seqanswers.com/forums/showthread.php?t=16842
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