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Search: Posts Made By: aleidenroth
Forum: Bioinformatics 02-01-2011, 12:50 AM
Replies: 9
Views: 14,930
Posted By aleidenroth
Hi, I had this issue, and after patching...

Hi,

I had this issue, and after patching bwa to the lastest update I run my sampe with

-r STR read group header line such as `@RG\tID:foo\tSM:bar' [null]

I specify ID, SM, LB and...
Forum: Bioinformatics 01-20-2011, 04:10 AM
Replies: 2
Views: 2,032
Posted By aleidenroth
I have the same problem, I also use bwa -r for...

I have the same problem, I also use bwa -r for alignment.

When I re-run TableRecalibrate with the added parameter

--default_read_group name_of_my_read_group

it seems to work and ignores the...
Forum: Bioinformatics 01-17-2011, 11:56 PM
Replies: 9
Views: 12,295
Posted By aleidenroth
Hi, Thanks a lot, I installed R and it works...

Hi,

Thanks a lot, I installed R and it works like a charm now!
Forum: Bioinformatics 01-17-2011, 04:15 AM
Replies: 9
Views: 12,295
Posted By aleidenroth
Picard: problem with Java?

Hi all,

I have the following problem when I run the Picard tool CollectInsertSizeMetrics.jar on a SAM file:

>java -jar
INPUT=alignedsorted.bam
OUTPUT=collectgcbiasmetricsoutfile ...
Forum: Sample Prep / Library Generation 12-07-2009, 02:34 AM
Replies: 8
Views: 14,266
Posted By aleidenroth
gel pic

Hi Hamid,

here's a gel pic. Conditions are as above except treatment 1 is 30 seconds sonication rather than 60s, and intensity is 5 rather than 8.

I think 25 cycles (12.5 minutes exposure)...
Forum: Sample Prep / Library Generation 12-04-2009, 12:27 AM
Replies: 8
Views: 14,266
Posted By aleidenroth
Hi Hamid, Thanks for the advice. I have...

Hi Hamid,

Thanks for the advice. I have switched to TC13 tubes. I know I should be using TC12 for 0.5ml volume, but at the moment we don't have a holder for those. Do you know if there's a glass...
Forum: Sample Prep / Library Generation 11-27-2009, 12:33 AM
Replies: 8
Views: 14,266
Posted By aleidenroth
Thanks both. @ECO We have tried the <1.5kb...

Thanks both.

@ECO
We have tried the <1.5kb conditions but got pretty big fragments.
I'll try and drop the intensity though. To get the time down, would you drop cycle time or cycle number?
...
Forum: Sample Prep / Library Generation 11-25-2009, 03:41 AM
Replies: 8
Views: 14,266
Posted By aleidenroth
Covaris S2: Chromatin shearing for ChIP(-seq?)

Hello everyone,

I'm new to this forum and have just started a PhD.

I'm planning to ChIP an epitope tagged protein (a transcription factor I'm expressing exogenously in transient transfections)....
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