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Forum: Bioinformatics 08-01-2019, 05:22 PM
Replies: 8
Views: 1,287
Posted By dcameron
Picards tools has no paper or preprint.

Picards tools has no paper or preprint.
Forum: Bioinformatics 03-30-2017, 04:27 PM
Replies: 3
Views: 2,175
Posted By dcameron
It's been by far the easiest approach I've found...

It's been by far the easiest approach I've found to SV annotation. My package isn't part of bioconductor yet as my linking between the two break-end for each breakpoint is just a $partner column and...
Forum: Bioinformatics 03-29-2017, 05:04 PM
Replies: 3
Views: 2,175
Posted By dcameron
It's not the cleanest approach for your purposes...

It's not the cleanest approach for your purposes but you can do:

breakdancer->VCF using https://github.com/PapenfussLab/sv_benchmark/blob/master/breakdancer2vcf.py

Then convert the VCFs (DELLY...
Forum: Bioinformatics 03-27-2017, 04:47 PM
Replies: 12
Views: 2,469
Posted By dcameron
I've raised an issue with the SAM specs here...

I've raised an issue with the SAM specs here (https://github.com/samtools/hts-specs/issues/197) to explicitly state that the regexes are POSIX basic regular expressions and the encoding is US-ASCII....
Forum: Bioinformatics 03-26-2017, 04:41 PM
Replies: 12
Views: 2,469
Posted By dcameron
The specs are indeed a bit light on detail. Not...

The specs are indeed a bit light on detail. Not only language, but character encoding is not specified. For VCF, I contributed a clarification that it is US-ASCII (technically headerless UTF-8 for...
Forum: Bioinformatics 03-23-2017, 04:39 PM
Replies: 12
Views: 2,469
Posted By dcameron
Given the SAM specifications...

Given the SAM specifications (https://samtools.github.io/hts-specs/SAMv1.pdf) disallow spaces in the RNAME field (Regular expression: "\*|[!-()+-<>-~][!-~]*"), it's unsurprising that downstream tools...
Forum: Bioinformatics 03-09-2017, 05:58 PM
Replies: 1
Views: 1,196
Posted By dcameron
I am somewhat confused by the question. A large...

I am somewhat confused by the question. A large amount of genomic and cancer research use NGS techniques as part of the research. NGS is a technique that can be applied to many areas of research....
Forum: Bioinformatics 02-26-2017, 09:30 PM
Replies: 0
Views: 685
Posted By dcameron
Introducing GRIDSS: the Genomic Rearrangement IDentification Software Suite

GRIDSS is typically used for detecting structural variation breakpoints but is a modular software suite containing a number of tools useful for the detection of genomic rearrangements. Whilst nowhere...
Forum: Bioinformatics 01-25-2017, 03:55 PM
Replies: 5
Views: 1,714
Posted By dcameron
As suggested by Markiyan, I strongly agree that...

As suggested by Markiyan, I strongly agree that you should benchmark your intended pipeline so you have an approximate estimate of your computational requirements. As soon as you get to the point...
Forum: Bioinformatics 01-25-2017, 03:33 PM
Replies: 2
Views: 2,500
Posted By dcameron
If you need to use bwa mem, you'll want to use...

If you need to use bwa mem, you'll want to use the -h and/or the -a command-line options but I don't think that'll do exactly what you're after. A number of other aligners can report in the manner...
Forum: Bioinformatics 12-21-2016, 04:59 PM
Replies: 3
Views: 2,932
Posted By dcameron
Firstly, since the underlying issue is a data...

Firstly, since the underlying issue is a data corruption issue, I would strongly recommend you re-download the corrupted data. As it is, your results will be not be reproducable from the original...
Forum: Bioinformatics 12-18-2016, 02:56 PM
Replies: 2
Views: 1,625
Posted By dcameron
I'm not quite sure what your workflow is that you...

I'm not quite sure what your workflow is that you would require a consensus from only a read pair and not be calling a consensus from the totality of reads at a given location but nevertheless, you...
Forum: Bioinformatics 12-06-2016, 02:08 PM
Replies: 11
Views: 7,711
Posted By dcameron
It's worked just like a native Ubuntu system for...

It's worked just like a native Ubuntu system for the basic bioinformatics pipelines (eg: sequence alignment through to variant calling) I've tried on it.

It's still a less transparent than a linux...
Forum: Bioinformatics 11-03-2016, 04:24 PM
Replies: 1
Views: 844
Posted By dcameron
The default settings for bowtie2 (bowtie2 --help)...

The default settings for bowtie2 (bowtie2 --help) are:
Reporting:
(default) look for multiple alignments, report best, with MAPQ


And the parameters that determine how thoroughly it...
Forum: Bioinformatics 11-01-2016, 11:09 PM
Replies: 8
Views: 3,786
Posted By dcameron
In that example can't you just take the assembled...

In that example can't you just take the assembled soft clipped bases as the consensus? If you take the final 117 bases of the assembly contig 'read'. The no-tools approach would be to right click on...
Forum: Bioinformatics 10-31-2016, 05:30 PM
Replies: 8
Views: 3,786
Posted By dcameron
Shameless plug: my structural variant caller...

Shameless plug: my structural variant caller GRIDSS (https://github.com/PapenfussLab/gridss/) performs genome-wide breakend assembly which, if you're looking for a turn-key solution to extend into...
Forum: Bioinformatics 10-31-2016, 05:15 PM
Replies: 8
Views: 3,786
Posted By dcameron
That does make sense as a simple starting point...

That does make sense as a simple starting point for filling the Ns. Code-wise, it's pretty simple and would look something like:


for each read
if cigar starts with S
replace S with...
Forum: Bioinformatics 10-30-2016, 09:35 PM
Replies: 8
Views: 3,786
Posted By dcameron
Since the read bases don't match, aren't you...

Since the read bases don't match, aren't you better off trimming the reads? What is your use case for considering mismatching bases aligned?
Forum: Bioinformatics 10-30-2016, 09:21 PM
Replies: 1
Views: 4,166
Posted By dcameron
It is defined in the SAM tags specifications...

It is defined in the SAM tags specifications (http://samtools.github.io/hts-specs/SAMtags.pdf) document which was split out from the main SAM specs at the end of last year.

Note that bwa can write...
Forum: Illumina/Solexa 02-08-2016, 09:40 PM
Replies: 1
Views: 2,287
Posted By dcameron
Have you done any adapter trimming? Alignment of...

Have you done any adapter trimming? Alignment of full-length reads is likely to result in soft clipped dovetailing reads. Since a significant portion of your library contains fragments shorter than...
Forum: Bioinformatics 01-14-2015, 07:10 PM
Replies: 6
Views: 1,882
Posted By dcameron
I would have thought using a soft-clip based SV...

I would have thought using a soft-clip based SV caller (local alignment required) would be more appropriate for single-end reads. A mean fragment untemplated sequence length of 0 with a variance of 0...
Forum: Bioinformatics 06-30-2014, 03:23 AM
Replies: 1
Views: 979
Posted By dcameron
What sort of structural variations are you hoping...

What sort of structural variations are you hoping to detect? Small indels within exons as well as retrocopied genes are detectable in exome sequencing data but the vast majority of structural...
Forum: Bioinformatics 01-20-2014, 10:10 PM
Replies: 6
Views: 3,464
Posted By dcameron
The picard tools utility BuildBamIndex can be run...

The picard tools utility BuildBamIndex can be run on Windows if you have java installed.

http://picard.sourceforge.net/command-line-overview.shtml#BuildBamIndex
Forum: Bioinformatics 01-20-2014, 10:07 PM
Replies: 3
Views: 2,026
Posted By dcameron
If the smaller files are being written, you might...

If the smaller files are being written, you might want to check if you are close to any limits on either available disk space or personal or group disk quota. Bwa doesn't have the most helpful error...
Forum: Bioinformatics 01-20-2014, 09:50 PM
Replies: 3
Views: 2,026
Posted By dcameron
Do you have write permission to the location bwa...

Do you have write permission to the location bwa want to write the index?

Also, bwa (at least for 0.7.5a) should autodetect which algorithm to use so -a bwtsw shouldn't be required.

Are any of...
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