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Forum: Bioinformatics 07-19-2016, 09:18 AM
Replies: 4
Views: 999
Posted By westerman
That is my guess. Not 100% sure though.

That is my guess. Not 100% sure though.
Forum: Bioinformatics 07-19-2016, 08:24 AM
Replies: 7
Views: 1,145
Posted By westerman
We have access to the University's "... large,...

We have access to the University's "... large, long-term, multi-tiered file caching and storage system utilizing both online disk and robotic tape drives. ..." Up to 10 PB on tape and 200 TB on...
Forum: Bioinformatics 07-19-2016, 08:03 AM
Replies: 4
Views: 999
Posted By westerman
I am not sure but I will make the, possibly...

I am not sure but I will make the, possibly unhelpful, suggestion to use Samtools 1.3 instead of 1.2. It may be more accurate and useful. From the change log:
Forum: Bioinformatics 06-16-2016, 07:14 AM
Replies: 4
Views: 888
Posted By westerman
Also look at the line above the line in question....

Also look at the line above the line in question. It may be causing a problem that continues to the troublesome line.

Like GenoMax I recommend reformat.sh
Forum: Bioinformatics 06-08-2016, 10:06 AM
Replies: 2
Views: 978
Posted By westerman
Talk to one of your system admins not to us.

Talk to one of your system admins not to us.
Forum: Illumina/Solexa 06-07-2016, 12:06 PM
Replies: 3
Views: 1,023
Posted By westerman
My general advice is to go with more PE reads --...

My general advice is to go with more PE reads -- the 'meat' of the assembly where it is nice to have a large coverage -- and fewer MP reads -- used to string the PE reads together with smaller...
Forum: SOLiD 05-24-2016, 11:43 AM
Replies: 15
Views: 5,157
Posted By westerman
Going off the topic here (which is that the SOLiD...

Going off the topic here (which is that the SOLiD is not good for denovo work) I wonder where you get that statement. It seems to me that 60 quality bases would be enough to place accurately except...
Forum: De novo discovery 05-18-2016, 10:09 AM
Replies: 1
Views: 1,979
Posted By westerman
The case for overlapping depends on the assembler...

The case for overlapping depends on the assembler you use. Which assembler to use not only depends on your species (what works well with a bacteria may not work well with a plant) but also on your...
Forum: Bioinformatics 05-17-2016, 09:20 AM
Replies: 5
Views: 519
Posted By westerman
Yes I asked NCBI. Their reply was " ... ....

Yes I asked NCBI. Their reply was " ... . Unfortunately, there is no viable option [to wwwblast] ..."
Forum: Bioinformatics 05-17-2016, 08:52 AM
Replies: 2
Views: 348
Posted By westerman
There might be a specific tool. Aside from...

There might be a specific tool. Aside from that, assuming you have your alignment in a BAM file then I see two methods.

1. Use the BedTools package and in particular coverageBed.

2. Use...
Forum: Bioinformatics 05-16-2016, 07:55 AM
Replies: 5
Views: 519
Posted By westerman
Blast+: mouse-over graphics

This is yet another iteration of a topic that has been raised over the years. Does anyone know of a good replacement for the mouse-over graphics produced by the (aging) wwwblast and also found on...
Forum: Bioinformatics 05-16-2016, 07:17 AM
Replies: 5
Views: 852
Posted By westerman
I agree with Mastal: both are useful. What is...

I agree with Mastal: both are useful. What is even more useful is to learn hoe to use the existing libraries in both languages. Instead of writing ones own code learn how to find and use...
Forum: Bioinformatics 04-18-2016, 08:39 AM
Replies: 3
Views: 880
Posted By westerman
ABySS, Ray, Platanus. I have found that...

ABySS, Ray, Platanus. I have found that Soapdenovo produces supposedly good statistics via shoving contigs together. Not always the case.
Forum: Bioinformatics 04-18-2016, 08:34 AM
Replies: 1
Views: 596
Posted By westerman
Using the variable 'o' for your R2 output file...

Using the variable 'o' for your R2 output file names. Nothing to do with trimmamatic but rather your script.
Forum: Bioinformatics 04-18-2016, 08:28 AM
Replies: 13
Views: 2,836
Posted By westerman
As a guess I think that the use of Ns in the...

As a guess I think that the use of Ns in the adapter file would cause problems since the program could match anything to those bases. But I am not sure about this.
Forum: General 04-14-2016, 07:42 AM
Replies: 5
Views: 1,355
Posted By westerman
Yes, I have tried. Did not work as of about 6...

Yes, I have tried. Did not work as of about 6 months ago.
Forum: Bioinformatics 03-28-2016, 12:44 PM
Replies: 3
Views: 827
Posted By westerman
I have always thought that invoking sed/awk or...

I have always thought that invoking sed/awk or any of the other programming tools for work inside Bash is ..., well, cheating. Useful in the practical "let us get stuff done" sense but at that...
Forum: Pacific Biosciences 03-24-2016, 01:08 PM
Replies: 20
Views: 4,066
Posted By westerman
PBJelly keeps crashing on me. Previous jobs...

PBJelly keeps crashing on me. Previous jobs (with potentially poor Illumina assemblies) produced poor results. That said I do have a current job that has been running for three days without...
Forum: Pacific Biosciences 03-24-2016, 12:33 PM
Replies: 20
Views: 4,066
Posted By westerman
All. Realistically it hard to tell which...

All.

Realistically it hard to tell which approach will work best. And to some extent it depends on how much time you have and the resources you already have on hand. In my case I will almost...
Forum: Bioinformatics 03-24-2016, 11:43 AM
Replies: 2
Views: 1,059
Posted By westerman
It is difficult to differentiate between zygosity...

It is difficult to differentiate between zygosity effects and duplications. In part it depends on the type of organism you are sequencing. Plants are notorious for duplications but then it can be...
Forum: Pacific Biosciences 03-24-2016, 11:35 AM
Replies: 20
Views: 4,066
Posted By westerman
Look at PacBio's hybrid assembly page: ...

Look at PacBio's hybrid assembly page:

https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/Large-Genome-Assembly-with-PacBio-Long-Reads

Given pre-existing Illumina-based...
Forum: Bioinformatics 03-22-2016, 07:36 AM
Replies: 2
Views: 591
Posted By westerman
Probably all of the OPT flags (field 12). ...

Probably all of the OPT flags (field 12). Official specifications are at:

https://samtools.github.io/hts-specs/SAMv1.pdf
Forum: Bioinformatics 03-09-2016, 09:11 AM
Replies: 42
Views: 4,065
Posted By westerman
That workflow should still be valid (although I...

That workflow should still be valid (although I have not run it). Basically (1) map the reads, (2) merge the reads that map, (3) merge the reads that do not map. I do not think that the method...
Forum: Bioinformatics 03-09-2016, 08:49 AM
Replies: 212
Views: 52,377
Posted By westerman
Also it seems to me that '-Xmx-211m' is odd. Why...

Also it seems to me that '-Xmx-211m' is odd. Why the negative 211? I am not sure that makes a difference but it might.
Forum: Illumina/Solexa 03-02-2016, 07:13 AM
Replies: 3
Views: 3,719
Posted By westerman
You can use both. Depends on the assembler.

You can use both. Depends on the assembler.
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