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Forum: Introductions 08-26-2015, 04:16 PM
Replies: 83
Views: 82,665
Posted By Jon_Keats
For those people following this thread. We...

For those people following this thread.

We are recruiting Post-Doctoral Fellows for one of our large cancer genomics programs. If you are interested in working in a cutting edge research...
Forum: Bioinformatics 03-16-2015, 09:51 PM
Replies: 2
Views: 2,211
Posted By Jon_Keats
What version of Salmon did you use? Have you...

What version of Salmon did you use? Have you posted to the google users board for sailfish/salmon? Rob is usually very good about getting answers to questions.

I agree with you somethings seems...
Forum: Introductions 11-25-2014, 10:09 PM
Replies: 83
Views: 82,665
Posted By Jon_Keats
Its been a very long time since I've updated this...

Its been a very long time since I've updated this thread. I've recently added a couple of new MAC computers that I use for development and tertiary analysis. And I wanted an updated build protocol...
Forum: RNA Sequencing 07-31-2014, 10:50 AM
Replies: 12
Views: 23,758
Posted By Jon_Keats
Also to install bedtools you will need to make a...

Also to install bedtools you will need to make a similar change

export LIBS = /usr/local/lib/libz.so.1.2.8
Forum: RNA Sequencing 07-26-2014, 08:53 PM
Replies: 12
Views: 23,758
Posted By Jon_Keats
Thanks Teja, Miss having you around

Thanks Teja,

Miss having you around
Forum: Bioinformatics 02-06-2014, 09:18 PM
Replies: 5
Views: 1,297
Posted By Jon_Keats
Are you sure you are not just reading into the...

Are you sure you are not just reading into the adaptor on the other end of the fragment?
Forum: RNA Sequencing 07-17-2013, 08:37 PM
Replies: 7
Views: 4,141
Posted By Jon_Keats
what read length, not bad if 100mers

what read length, not bad if 100mers
Forum: Illumina/Solexa 07-17-2013, 08:30 PM
Replies: 9
Views: 3,831
Posted By Jon_Keats
Kapa works the best of all things we have tested....

Kapa works the best of all things we have tested. TruSeqDNA, Agilent XT, Agilent XT2, NEB Ultra. Oddly Agilent XT2 actually worked best at 500ng. If you want our protocol see www.keatslab.org
Forum: Sample Prep / Library Generation 06-18-2013, 12:32 PM
Replies: 7
Views: 61,424
Posted By Jon_Keats
Great thread Phillip, These are exactly many...

Great thread Phillip,

These are exactly many issues I've encountered in the past. My lab it actually told to set the nanodrop vertical bar at 270 to make sure the peak absorbance is not at 270. ...
Forum: General 06-12-2013, 09:44 PM
Replies: 33
Views: 9,443
Posted By Jon_Keats
Hi Shi, Just wanted to thank you this last...

Hi Shi,

Just wanted to thank you this last patch seems to be much improved. Now moving on to test featureCounts.
Forum: General 06-09-2013, 11:02 PM
Replies: 33
Views: 9,443
Posted By Jon_Keats
Running a test tonight...

Running a test tonight...
Forum: Bioinformatics 06-09-2013, 10:53 PM
Replies: 8
Views: 6,467
Posted By Jon_Keats
Agilent adaptors are exactly the same as the...

Agilent adaptors are exactly the same as the illumina truseq less the 8bp barcode in the case of XT2 adaptors replaces the 6bp barcode in truseq. Ultimately there is little room for changes as there...
Forum: General 06-06-2013, 10:49 PM
Replies: 33
Views: 9,443
Posted By Jon_Keats
Didn't happen in the previous version so I'm...

Didn't happen in the previous version so I'm guessing its a result of the fix they put in for my last issue. I'm impressed with how fast they are turning around fixes so it makes it worth the effort.
Forum: Bioinformatics 06-06-2013, 10:27 PM
Replies: 44
Views: 30,065
Posted By Jon_Keats
We have done a decent bit of side by side...

We have done a decent bit of side by side comparisons of STAR 2.3.0 and TOPHAT 2.0.8b.

Short story is they are not very different. On most obvious counts STAR wins, faster and more unique...
Forum: General 06-06-2013, 10:10 PM
Replies: 33
Views: 9,443
Posted By Jon_Keats
Hi Wei, Got a new bug during SAM->BAM...

Hi Wei,

Got a new bug during SAM->BAM conversion using samtools:
[samopen] SAM header is present: 178 sequences.
Parse error at line 580: sequence and quality are inconsistent

I pulled out...
Forum: Bioinformatics 06-06-2013, 09:57 PM
Replies: 5
Views: 2,248
Posted By Jon_Keats
Nizar, it will run on just the Tumor/normal DNA...

Nizar, it will run on just the Tumor/normal DNA bam, RNA bam files are NOT required.
Forum: Bioinformatics 06-06-2013, 09:54 PM
Replies: 5
Views: 2,248
Posted By Jon_Keats
Great Job Alexis, first runs with the new version...

Great Job Alexis, first runs with the new version are coming off right now... Looks great as always
Forum: General 06-05-2013, 09:58 PM
Replies: 33
Views: 9,443
Posted By Jon_Keats
Thanks, running at test now. I'll let you know...

Thanks, running at test now. I'll let you know how it goes
Forum: General 06-04-2013, 11:46 PM
Replies: 33
Views: 9,443
Posted By Jon_Keats
Assuming Wei can confirm that is correct. I...

Assuming Wei can confirm that is correct. I actually understand your explanation, so thanks @sdriscoll

So if we were to set it dynamically to include read pairs within 1 standard deviation it...
Forum: General 06-04-2013, 11:04 PM
Replies: 33
Views: 9,443
Posted By Jon_Keats
So by --mindist does this really mean the...

So by --mindist does this really mean the sequence length that is sequenced by both read1 and read2?

I only pick on this as it was a MAJOR issue in Tophat as read lengths increased and we started...
Forum: Sample Prep / Library Generation 06-04-2013, 08:58 PM
Replies: 35
Views: 20,477
Posted By Jon_Keats
We are testing the Agilent stranded kit in the...

We are testing the Agilent stranded kit in the next couple of weeks. I'll try to get back to this thread to mention the outcome. Good to see ETHANol again.
Forum: RNA Sequencing 06-04-2013, 08:45 PM
Replies: 9
Views: 13,717
Posted By Jon_Keats
We include the ERCC in most experiments now. We...

We include the ERCC in most experiments now. We see 0.2-1.5% of all reads coming from the spike-ins. Personally I see a significant amount of value in these reagents and I highly recommend them to...
Forum: General 06-03-2013, 10:33 PM
Replies: 33
Views: 9,443
Posted By Jon_Keats
Thanks for the prompt response. I don't...

Thanks for the prompt response.

I don't understand how you get 49

Read 1------------------------->
Fragment --------------------------------------------------
...
Forum: Bioinformatics 06-03-2013, 10:14 PM
Replies: 4
Views: 1,858
Posted By Jon_Keats
See...

See http://www.broadinstitute.org/gatk/guide/topic?name=methods-and-workflows#Introduction

Look about half way down for lift-over
Forum: General 06-01-2013, 11:20 PM
Replies: 33
Views: 9,443
Posted By Jon_Keats
For subjunc analysis I'm a bit confused by the...

For subjunc analysis I'm a bit confused by the following parameters:

-d --mindist <int> the minimum distance between two reads in a pair, 50 by default
-D --maxdist <int> the...
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