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Search: Posts Made By: PeteH
Forum: Bioinformatics 04-17-2014, 09:31 PM
Replies: 16
Views: 6,443
Posted By PeteH
Thanks, Brent. Sorry, I'd misinterpreted your...

Thanks, Brent. Sorry, I'd misinterpreted your statement as saying that you thought bismark_methylation_extractor didn't give sane results. All good :)
Forum: Bioinformatics 04-17-2014, 04:31 PM
Replies: 16
Views: 6,443
Posted By PeteH
Can you please elaborate on this, Brent? ...

Can you please elaborate on this, Brent?
Cheers,
Pete
Forum: Bioinformatics 03-25-2014, 02:22 PM
Replies: 649
Views: 172,279
Posted By PeteH
Hi Felix, A seemingly harmless error is...

Hi Felix,

A seemingly harmless error is raised right at the end of running the methylation extractor with the --mbias_only flag (v0.10.1):

bismark_methylation_extractor -p --mbias_only...
Forum: Bioinformatics 03-05-2014, 04:22 PM
Replies: 649
Views: 172,279
Posted By PeteH
Fantastic, thanks Felix! Simply having a second...

Fantastic, thanks Felix! Simply having a second hash storing the SQ_order was so much simpler than my idea.
Forum: Bioinformatics 03-04-2014, 08:27 PM
Replies: 649
Views: 172,279
Posted By PeteH
Hi Felix, Currently the SAM header produced...

Hi Felix,

Currently the SAM header produced by Bismark has the @SQ fields in a more-or-less random order. This means that the @SQ fields will almost certainly not be in the same order as the they...
Forum: Bioinformatics 01-19-2014, 02:29 PM
Replies: 6
Views: 2,728
Posted By PeteH
Hi Lintao, I didn't receive your private...

Hi Lintao,

I didn't receive your private message. Nevertheless, I should make it clear that the version of the software that I was sent still does not work.

Cheers,
pete
Forum: Bioinformatics 10-27-2013, 03:19 PM
Replies: 17
Views: 4,145
Posted By PeteH
There are known problems with Mavericks and...

There are known problems with Mavericks and RStudio (http://blog.rstudio.org/2013/10/22/rstudio-and-os-x-10-9-mavericks/). R itself is fine but it's something to bear in mind if you use RStudio and...
Forum: Bioinformatics 10-12-2013, 12:15 AM
Replies: 10
Views: 5,572
Posted By PeteH
Ah, as the data are non-human this may require...

Ah, as the data are non-human this may require some extra work. Posting a small subset of your annotation and VCF file, along with the code used to generate it, will likely assist people to help you....
Forum: Bioinformatics 10-11-2013, 04:19 PM
Replies: 10
Views: 5,572
Posted By PeteH
Have you read and followed the instructions in...

Have you read and followed the instructions in the Quick Start Guide (http://bioinf.wehi.edu.au/software/linkdatagen/MPS%20linkage%20quick%20start.doc) and Documentation...
Forum: Bioinformatics 10-09-2013, 02:26 PM
Replies: 10
Views: 5,572
Posted By PeteH
You might like to try LINKDATAGEN...

You might like to try LINKDATAGEN (http://bioinf.wehi.edu.au/software/linkdatagen/#mps) to convert your VCF file into input files for linkage programs such as MERLIN...
Forum: Bioinformatics 08-20-2013, 05:51 PM
Replies: 649
Views: 172,279
Posted By PeteH
The --no_overlap option is for paired-end...

The --no_overlap option is for paired-end libraries, regardless of whether they are directional or non-directional. Basically, you don't want to "double count" methylation calls from any overlapping...
Forum: Bioinformatics 08-16-2013, 07:53 PM
Replies: 649
Views: 172,279
Posted By PeteH
The new HTML reports are very slick!

The new HTML reports are very slick!
Forum: Bioinformatics 08-07-2013, 04:34 PM
Replies: 5
Views: 1,713
Posted By PeteH
You'll need to clarify your question, perhaps...

You'll need to clarify your question, perhaps with an example of such a CpG.
Forum: Bioinformatics 07-29-2013, 12:50 AM
Replies: 649
Views: 172,279
Posted By PeteH
Thanks for the new tar file. There's some issue...

Thanks for the new tar file. There's some issue with the archive utility on my macbook because it works fine for me on other machines but not on my macbook. Sorry for the confusion.

The...
Forum: Bioinformatics 07-26-2013, 08:52 PM
Replies: 649
Views: 172,279
Posted By PeteH
Thanks for incorporate those changes, Felix. One...

Thanks for incorporate those changes, Felix. One thing, you've got the CTOT and CTOB flags swapped around in that table. They should be:

new default ...
Forum: Bioinformatics 07-25-2013, 09:00 PM
Replies: 649
Views: 172,279
Posted By PeteH
I should emphasise, that it is only for...

I should emphasise, that it is only for paired-end data that the SAM/BAM needs to be sorted by queryname order. If you have single-end data then it won't matter whether the SAM/BAM is sorted by...
Forum: Bioinformatics 07-24-2013, 08:28 PM
Replies: 649
Views: 172,279
Posted By PeteH
It's probably worth noting in the documentation...

It's probably worth noting in the documentation that bismark_methylation_extractor expects that for paired-end data that the reads are in queryname order, i.e. the same ordering scheme that Bismark...
Forum: Bioinformatics 07-24-2013, 08:24 PM
Replies: 649
Views: 172,279
Posted By PeteH
Thanks, Felix. My (brief) testing suggests there...

Thanks, Felix. My (brief) testing suggests there are no problems except that M-bias text file isn't written to the directory given by the "--output" flag, but rather is written to the current working...
Forum: Bioinformatics 07-18-2013, 03:02 AM
Replies: 649
Views: 172,279
Posted By PeteH
Agreed. I'm having a closer look at M-bias as a...

Agreed. I'm having a closer look at M-bias as a colleague suggested most of the 3' M-bias he had observed in his data was simply due to the inherent decline in quality of base calls at the 3' end of...
Forum: Bioinformatics 07-18-2013, 02:38 AM
Replies: 649
Views: 172,279
Posted By PeteH
1) Great, I can retire my (slow) Python script! ...

1) Great, I can retire my (slow) Python script!
2) True, however Kasper Hansen convinced me of the benefit of this level of stratification in M-bias plots (see e.g. Figure 2b of Hansen, K. D.,...
Forum: Bioinformatics 07-17-2013, 05:39 PM
Replies: 649
Views: 172,279
Posted By PeteH
I'm very happy to see the M-bias feature added to...

I'm very happy to see the M-bias feature added to Bismark! Especially because it is better than my own basic implementation of this idea and thus saves me the trouble of refining mine :)

I've had...
Forum: Bioinformatics 04-28-2013, 03:53 PM
Replies: 3
Views: 15,820
Posted By PeteH
You might like to have a read of this paper as a...

You might like to have a read of this paper as a starter - Tackling the widespread and critical impact of batch effects in high-throughput data (http://www.ncbi.nlm.nih.gov/pubmed/?term=20838408) ...
Forum: Epigenetics 04-24-2013, 04:36 PM
Replies: 3
Views: 1,856
Posted By PeteH
To clarify, are you wanting to identify cytosines...

To clarify, are you wanting to identify cytosines that show evidence of methylation and thus you want to filter out any with low estimated levels of methylation that you think might be simply...
Forum: Introductions 04-16-2013, 04:14 AM
Replies: 1
Views: 881
Posted By PeteH
Hi Pat, I think you're right to be...

Hi Pat,

I think you're right to be suspicious of this result. I know that many studies using the 450k or 27k arrays filter out probes that overlap with known SNPs due to the confounding that you...
Forum: Bioinformatics 02-28-2013, 12:56 PM
Replies: 7
Views: 2,968
Posted By PeteH
That sounds useful to me; care to share your...

That sounds useful to me; care to share your script for creating these?
Thanks,
Pete
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