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Forum: RNA Sequencing 01-22-2014, 12:18 AM
Replies: 5
Views: 2,457
Posted By HGENETIC
Thanks for that, really appreciate it!

Thanks for that, really appreciate it!
Forum: RNA Sequencing 01-17-2014, 12:52 AM
Replies: 5
Views: 2,457
Posted By HGENETIC
Thanks Bukowski for your reply. The aim for this...

Thanks Bukowski for your reply. The aim for this experiment is to see if there are specific genes/biological pathways that are massively up regulated in these tumours, some mouse work has identified...
Forum: RNA Sequencing 01-16-2014, 07:37 AM
Replies: 5
Views: 2,457
Posted By HGENETIC
No control for tumour RNA-seq data

Hi all,

I'm trying to set up an RNAseq experiment looking at gene expression in brain tumour samples. This is a pilot experiment and we only have 5 tumour samples to work with but I'm not sure...
Forum: Sample Prep / Library Generation 03-09-2012, 12:26 AM
Replies: 41
Views: 25,799
Posted By HGENETIC
Hi Genquest, we had a similar situation to...

Hi Genquest,

we had a similar situation to yours in that our qPCR results gave higher DNA concentration than our picogreen (see post above for qPCR kit used). However, when ouor sequence provider...
Forum: Bioinformatics 01-25-2012, 03:19 AM
Replies: 0
Views: 2,288
Posted By HGENETIC
picard add read groups

Hi all,

I've been trying to get around this problem for the last couple of days and |I haven't been able to do anything myself and haven't seen any solutions in any forums. Here's my problem:
My...
Forum: Bioinformatics 01-19-2012, 09:05 AM
Replies: 17
Views: 5,110
Posted By HGENETIC
The GATK manual seems to use the b37 data and in...

The GATK manual seems to use the b37 data and in some work we've done in collaboration with the Broad they've used that as well so if it's good enough for them it's good enough for me. I'd still like...
Forum: Bioinformatics 01-19-2012, 05:37 AM
Replies: 17
Views: 5,110
Posted By HGENETIC
Out of curiosity do you know the difference...

Out of curiosity do you know the difference between the data in the GATK bundle for b37 and hg19, all the file names are the same except for this?
Forum: Bioinformatics 01-19-2012, 05:31 AM
Replies: 17
Views: 5,110
Posted By HGENETIC
Thanks for that I think that would work nicely,...

Thanks for that I think that would work nicely, the reason I removed the chr tags was because i was trying to use the dbSNP135 known variant file which only had intergers whereas my fasta file had...
Forum: Bioinformatics 01-19-2012, 05:02 AM
Replies: 17
Views: 5,110
Posted By HGENETIC
I'm relatively new to UNIX and so for me the...

I'm relatively new to UNIX and so for me the easiest way to overcome the problem was to make everything into an interger, how would you convert chromosomal intergers in a .vcf or .fasta file back...
Forum: Bioinformatics 01-19-2012, 03:17 AM
Replies: 17
Views: 5,110
Posted By HGENETIC
I just used the UNIX command: $ sed...

I just used the UNIX command:

$ sed "s/chr//g" file_to.change > new.file

try that it worked for me.
Forum: Bioinformatics 01-19-2012, 02:52 AM
Replies: 17
Views: 5,110
Posted By HGENETIC
GATK realignment

Hi there,
I'm trying to produce a list of possible indels using the GATK Realigner Target Creator. I have the latest version of hg19.fasta as my reference and db135.vcf file as my known indels file....
Forum: Sample Prep / Library Generation 11-14-2011, 02:56 AM
Replies: 2
Views: 1,918
Posted By HGENETIC
Thanks nickloman, that's a relief!!

Thanks nickloman, that's a relief!!
Forum: Sample Prep / Library Generation 11-14-2011, 02:37 AM
Replies: 2
Views: 1,918
Posted By HGENETIC
TruSeq library size

Hi all,

I'm setting up a library prep using TruSeq DNA sample enrichment kits, I've sheared the DNA using Covaris and have run the product on a bioanalyzer. My library peaks seem to be around the...
Forum: Sample Prep / Library Generation 10-04-2011, 12:07 AM
Replies: 2
Views: 2,257
Posted By HGENETIC
It's for a targeted capture protocol using an...

It's for a targeted capture protocol using an NimbleGen probe library so basically it's very similar.
Forum: Sample Prep / Library Generation 10-03-2011, 07:07 AM
Replies: 41
Views: 25,799
Posted By HGENETIC
We've always used picogreen and found it matches...

We've always used picogreen and found it matches well with the qbit results that our sequence service provider uses to make library dilutions before running. However, after some curious results we...
Forum: Sample Prep / Library Generation 10-03-2011, 06:26 AM
Replies: 2
Views: 2,257
Posted By HGENETIC
phosphorothioate bond

Hi, does anyone have experience of using blocking primers during a hybridisation step without including a phosphorothioate bond? I ordered some primers for use with TruSeq but forgot to add this bond...
Forum: Illumina/Solexa 09-29-2011, 03:12 AM
Replies: 145
Views: 319,596
Posted By HGENETIC
Wink Thanks for posting this it's really helpful and...

Thanks for posting this it's really helpful and is something I'd been trying to fathom out myself recently - H
Forum: Sample Prep / Library Generation 09-28-2011, 01:32 AM
Replies: 0
Views: 1,466
Posted By HGENETIC
Tru-Seq in-line controls

Hi all, I'm going to be setting up a Tru-seq DNA sample preparation assay soon and just wondered if people generally use the in-line controls or not and whether there are any potential pitfalls I...
Forum: Sample Prep / Library Generation 09-06-2011, 05:11 AM
Replies: 8
Views: 5,552
Posted By HGENETIC
We tried using this enzyme, we had it automated...

We tried using this enzyme, we had it automated on a Biomek Fx and it seemed to work OK the first time we did the expt. Then we repeated everything using some 48 samples and everything failed, I...
Forum: Sample Prep / Library Generation 08-31-2011, 04:34 AM
Replies: 18
Views: 26,738
Posted By HGENETIC
Great stuff, thanks jakeenk..

Great stuff, thanks jakeenk..
Forum: Sample Prep / Library Generation 08-30-2011, 01:58 AM
Replies: 0
Views: 1,349
Posted By HGENETIC
Massive over-representation of barcodes

Hi, I've been trying to get a protocol automated using pooled samples and indexing. We've had some initial success when performing library prep on individual samples and pooling postcapture and...
Forum: Sample Prep / Library Generation 08-30-2011, 01:43 AM
Replies: 18
Views: 26,738
Posted By HGENETIC
Do you happen to have a pdf of this as I don't...

Do you happen to have a pdf of this as I don't have a password to access the full text?

Cheers - H
Forum: Illumina/Solexa 04-11-2011, 05:29 AM
Replies: 19
Views: 6,687
Posted By HGENETIC
No we've only used solution based capture

No we've only used solution based capture
Forum: Illumina/Solexa 04-08-2011, 07:52 AM
Replies: 19
Views: 6,687
Posted By HGENETIC
We have used the Nimblegen solution based capture...

We have used the Nimblegen solution based capture method on a target region of ~1.5Mb. Our first expt screwed up fantastically well so we've had to repeat everything from scratch and are in the...
Forum: Sample Prep / Library Generation 10-21-2010, 07:09 AM
Replies: 5
Views: 3,393
Posted By HGENETIC
Is this a known problem with BGI and in what way...

Is this a known problem with BGI and in what way is the data garbage? Not sent anything there but some other collaborators have so it would be interesting to know what sort of output they are giving...
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