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Search: Posts Made By: davidblaney
Forum: Bioinformatics 11-20-2013, 02:49 AM
Replies: 6
Views: 6,435
Posted By davidblaney
I was thinking a memory issue when I first read...

I was thinking a memory issue when I first read this. Have a look at the requirement on there website. Failing that drop them an email. :)
Forum: Bioinformatics 11-11-2013, 03:29 AM
Replies: 7
Views: 3,220
Posted By davidblaney
I am going to try these new methods out, thanks.

I am going to try these new methods out, thanks.
Forum: Bioinformatics 11-07-2013, 12:34 AM
Replies: 7
Views: 3,220
Posted By davidblaney
Hi, The FPKM values for the genes are a sum...

Hi,

The FPKM values for the genes are a sum of the FPKM values found for transcripts of that gene... so I guess you could expect differing values come from the difference in transcripts and the...
Forum: Bioinformatics 10-11-2013, 02:39 AM
Replies: 1
Views: 1,698
Posted By davidblaney
Hi, I'm guessing that you would like to see...

Hi,

I'm guessing that you would like to see progress of the bwa aln command.
I looked into this before for version 0.6.2 of bwa and found every so often the program will print this information....
Forum: Bioinformatics 09-09-2013, 01:52 AM
Replies: 24
Views: 25,850
Posted By davidblaney
Got this error when my machine didn't have enough...

Got this error when my machine didn't have enough free memory.

Hope this helps someone
Forum: Bioinformatics 08-05-2013, 07:19 AM
Replies: 5
Views: 9,540
Posted By davidblaney
Is this what you are looking for? ...

Is this what you are looking for?

http://genomebiology.com/2013/14/7/R80/abstract
Forum: Bioinformatics 04-04-2013, 08:04 AM
Replies: 3
Views: 6,221
Posted By davidblaney
I have used windows Power Shell to manipulate big...

I have used windows Power Shell to manipulate big files on occasion, this is a crude way to get first and second 100 reads. Only really suitable for simple splitting.




PS> Get-Content...
Forum: Bioinformatics 04-02-2013, 03:37 AM
Replies: 2
Views: 1,363
Posted By davidblaney
Hi, After looking at CPAN and then at the...

Hi,

After looking at CPAN and then at the module code directly it looks as if mpileup is not supported as there is no '-command' option in the code.

This may be because the module was written...
Forum: Bioinformatics 03-31-2013, 05:24 AM
Replies: 6
Views: 3,090
Posted By davidblaney
No worries, This is a good paper to help...

No worries,

This is a good paper to help with analysis using cummbeRbund also.

http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html
Forum: Bioinformatics 03-31-2013, 04:07 AM
Replies: 1
Views: 1,045
Posted By davidblaney
If you could post a few lines of your VCF on here...

If you could post a few lines of your VCF on here or email them to me I can have a go at helping you out.

David
Forum: Bioinformatics 03-31-2013, 04:04 AM
Replies: 4
Views: 2,354
Posted By davidblaney
Hi, Have you tried backslash before it: ...

Hi,

Have you tried backslash before it:

(1.0 \* DP)

or using single quotes around the expression?
Forum: Bioinformatics 03-28-2013, 07:37 AM
Replies: 6
Views: 3,090
Posted By davidblaney
Yes I have tried those packages before. I also...

Yes I have tried those packages before. I also like Picards tool set for alignment metrics such as



http://picard.sourceforge.net/command-line-overview.shtml

I guess the question to ask...
Forum: Bioinformatics 03-27-2013, 08:07 AM
Replies: 1
Views: 1,388
Posted By davidblaney
The Estimated number of unique fragments in your...

The Estimated number of unique fragments in your sequenced library.

it uses this (from the API documentation)
Forum: Bioinformatics 03-25-2013, 04:41 AM
Replies: 6
Views: 3,090
Posted By davidblaney
So to get 'mappable reads' I would look at the...

So to get 'mappable reads' I would look at the first output which is the read stats.

---
(1) 19231140 reads; of these:
(2) 19231140 (100.00%) were paired; of these:
(3) 1790875 (9.31%) aligned...
Forum: Bioinformatics 03-25-2013, 04:24 AM
Replies: 14
Views: 4,549
Posted By davidblaney
Hi, As toby said giving examples would be...

Hi,

As toby said giving examples would be more helpful.

When using perl you should always use


use warnings;
use strict;
Forum: RNA Sequencing 05-21-2012, 05:21 AM
Replies: 1
Views: 2,678
Posted By davidblaney
Hi Kumardeep, Could it be that you left out...

Hi Kumardeep,

Could it be that you left out gtf_to_sam from you PATH?

the code looks light it might be something to do with this.

David
Forum: Bioinformatics 05-09-2012, 07:22 AM
Replies: 4
Views: 2,476
Posted By davidblaney
Any luck

Hi,

I'm looking for a similar kind of data set and just wondered if you had any luck?

Thanks
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