SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 27
Search took 0.00 seconds.
Search: Posts Made By: ieuanclay
Forum: Bioinformatics 08-23-2010, 04:09 AM
Replies: 3
Views: 2,472
Posted By ieuanclay
Thanks for the tip, I hadn't been through...

Thanks for the tip, I hadn't been through Bioconductor yet.
Forum: Bioinformatics 08-23-2010, 03:13 AM
Replies: 3
Views: 2,472
Posted By ieuanclay
High throughput Gene Ontology enrichment API

A bioinformatics question: I have been doing more and more Gene Ontology (GO) work, specifically, I am looking for enriched terms in my various gene sets. I usually go through the web-based programs...
Forum: RNA Sequencing 07-07-2009, 03:22 AM
Replies: 9
Views: 11,324
Posted By ieuanclay
Check the forums here for TopHat if you want to...

Check the forums here for TopHat if you want to know about mapping RNAseq!

The actual way that you map is very dependent on the source of your RNA, so i would need to know more about your...
Forum: Illumina/Solexa 07-06-2009, 07:43 AM
Replies: 3
Views: 1,721
Posted By ieuanclay
I suspect you have contaminated samples then. The...

I suspect you have contaminated samples then. The primer dimers, when you get them, are very clearly that... It is important to avoid any kind of contamination - unclean razor blades, cross...
Forum: Illumina/Solexa 07-06-2009, 04:34 AM
Replies: 3
Views: 1,721
Posted By ieuanclay
Was it a totally independent blank control? i.e....

Was it a totally independent blank control? i.e. a water control for the PCR?
You may simply be looking at primer dimers - what size was your 'contamination'?

A good idea (at least for peace of...
Forum: Academic/Non-Profit Jobs 06-26-2009, 06:24 AM
Replies: 7
Views: 2,979
Posted By ieuanclay
Yeah - but I want to get out of here!! I have...

Yeah - but I want to get out of here!! I have been here too long and my feet are getting itchy...
Forum: Epigenetics 06-25-2009, 02:02 AM
Replies: 13
Views: 6,791
Posted By ieuanclay
40-60% using the default ELAND settings is a...

40-60% using the default ELAND settings is a little on the low side for 36bp (paired end?). If you want to try alternate settings, bowtie (see the forum here) is very amenable to messing around with...
Forum: Academic/Non-Profit Jobs 06-22-2009, 03:19 AM
Replies: 7
Views: 2,979
Posted By ieuanclay
Has anyone heard anything about Berlin? I think...

Has anyone heard anything about Berlin? I think Pfizer just moved their HQ there, so there might be upcoming opportunities... Any other companies/hospitals/institutes worth a look?
Forum: Academic/Non-Profit Jobs 06-18-2009, 07:19 AM
Replies: 7
Views: 2,979
Posted By ieuanclay
I am actually off to Barcelona next month, so I...

I am actually off to Barcelona next month, so I will check it out!

I have also heard Berlin is becoming something of a biotech hub - does anyone know of good companies/institutes to look at?
Forum: Academic/Non-Profit Jobs 06-18-2009, 03:14 AM
Replies: 7
Views: 2,979
Posted By ieuanclay
Looking for advice on european genomics

Hi All,

I am in the final year of my PhD and starting to get a little worried about what I am going to do next...:confused:

I don't think I want to do a postdoc, but I love what I do...
Forum: Bioinformatics 06-16-2009, 09:03 AM
Replies: 513
Views: 187,530
Posted By ieuanclay
I'll have a look, and no i don't mind sharing, as...

I'll have a look, and no i don't mind sharing, as long as you promise not to laugh!

Ieuan
Forum: Bioinformatics 06-16-2009, 06:02 AM
Replies: 513
Views: 187,530
Posted By ieuanclay
Great, thanks. I am writing an old skool perl GUI...

Great, thanks. I am writing an old skool perl GUI wrapper to handle all the input and forking off several alignment runs (separate from the internal forking that bowtie already does, i.e. if i want...
Forum: Bioinformatics 06-15-2009, 11:30 AM
Replies: 513
Views: 187,530
Posted By ieuanclay
also, i just noticed a typo in the manual...

also, i just noticed a typo in the manual (0.9.9.3) : for the --fr/rf/ff docs, you call --ff --ll. Maybe this isn't a typo and i am just being really dumb...

Ieuan
Forum: Bioinformatics 06-15-2009, 11:18 AM
Replies: 513
Views: 187,530
Posted By ieuanclay
Hi Ben, Quick question - if you supply...

Hi Ben,

Quick question - if you supply paired end arguments (--ff / -I / etc...) , but only supply a <singles> file (not <mates1/2>), will the PE args just be ignored?

Similarly, if I specify...
Forum: Epigenetics 06-08-2009, 04:07 AM
Replies: 20
Views: 56,916
Posted By ieuanclay
might want to add PeakSeq too: ...

might want to add PeakSeq too:

http://www.nature.com/nbt/journal/v27/n1/full/nbt.1518.html

Not earth-shattering, but i think their advice on normalising to input is really worthwhile.
Forum: RNA Sequencing 06-04-2009, 02:44 AM
Replies: 36
Views: 23,225
Posted By ieuanclay
We tried the ribominus kit and it worked well - I...

We tried the ribominus kit and it worked well - I would agree with doxologist though, you need good quality! It is a good alterantive if you want to remove rRNA whilst not avoiding not polyA'd RNAs...
Forum: RNA Sequencing 06-04-2009, 02:41 AM
Replies: 9
Views: 11,324
Posted By ieuanclay
Hi all, We have had success with PE RNAseq...

Hi all, We have had success with PE RNAseq (illumina).

Some of the main pitfalls that we found:
-when you make your cDNA, if you use random hexamers (best results for us), your first strand...
Forum: Bioinformatics 04-07-2009, 02:48 AM
Replies: 513
Views: 187,530
Posted By ieuanclay
Hi Ben, I have seen this in 0.9.9 and...

Hi Ben,

I have seen this in 0.9.9 and 0.9.9.1 (x64), m.musculus ncbi36 and 37 indices (offrates 2,3,4,5). Args were -q --solexa-quals -a --unfq ... -p 2/3/6 . Input was only ~1/2 Mb of fastq...
Forum: Bioinformatics 04-06-2009, 11:42 AM
Replies: 513
Views: 187,530
Posted By ieuanclay
Hi Ben, Thanks for your advice earlier,...

Hi Ben,

Thanks for your advice earlier, post-processing of results is now working well!

However I have found that using --all isn't a problem, until i specify --nostrata as well which causes...
Forum: Bioinformatics 03-13-2009, 06:59 AM
Replies: 4
Views: 2,335
Posted By ieuanclay
No worries - even if you don't use their...

No worries - even if you don't use their software, the lessons learned still apply.

Ieuan
Forum: Bioinformatics 03-13-2009, 06:51 AM
Replies: 4
Views: 2,335
Posted By ieuanclay
Hi, A very good paper came out recently :...

Hi,

A very good paper came out recently : "PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls" Rozowsky et al Nat. Biotech. (2009) 27(1):66-

It answers a lot of...
Forum: Bioinformatics 03-11-2009, 06:33 AM
Replies: 513
Views: 187,530
Posted By ieuanclay
Hi Ben, Thanks for your help so far - I am...

Hi Ben,

Thanks for your help so far - I am relatively new to mapping (but not so new that I am not impressed by bowtie!), so please excuse any dopey questions...

My worry is that I will lose...
Forum: Bioinformatics 03-10-2009, 11:48 AM
Replies: 513
Views: 187,530
Posted By ieuanclay
Sorry to keep on about this, I just want to get...

Sorry to keep on about this, I just want to get it clear.

By default:
-k is 1, so only one (the best according -n-v-l-e) alignment is reported.
-m is unlimited

so if a read has multiple...
Forum: Bioinformatics 03-10-2009, 09:35 AM
Replies: 513
Views: 187,530
Posted By ieuanclay
Yes - great thank you! Ieuan

Yes - great thank you!

Ieuan
Forum: Bioinformatics 03-10-2009, 08:35 AM
Replies: 513
Views: 187,530
Posted By ieuanclay
Doh... Your patience obviously exceeds mine... ...

Doh... Your patience obviously exceeds mine...

I was confused by the default for -m being unlimited - does this mean that without --maxfa being set, your mapped output will include sequences with...
Showing results 1 to 25 of 27

 


All times are GMT -8. The time now is 05:28 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO