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Search: Posts Made By: Lee Sam
Forum: Bioinformatics 06-28-2013, 12:20 PM
Replies: 6
Views: 1,870
Posted By Lee Sam
We discussed this a little while back and I think...

We discussed this a little while back and I think it's really a question of what application you're trying to accelerate, and whether that task has been something that has had effort invested to...
Forum: Bioinformatics 04-05-2012, 10:46 AM
Replies: 16
Views: 7,287
Posted By Lee Sam
Has anyone figured this issue out? I'm running a...

Has anyone figured this issue out? I'm running a small study with cancer samples and I don't even see TP53 annotated in the genes.fpkm_tracking using either the Illumina-provided UCSC or Ensembl...
Forum: Illumina/Solexa 12-13-2010, 10:36 AM
Replies: 17
Views: 7,076
Posted By Lee Sam
Sorry, I should have been more clear. 100 million...

Sorry, I should have been more clear. 100 million paired reads (or 200 million ends).
Forum: Helicos / Direct Genomics 11-30-2010, 01:44 PM
Replies: 18
Views: 14,314
Posted By Lee Sam
I'm really interested in seeing what PacBio can...

I'm really interested in seeing what PacBio can output for RNA-Seq since their sequencing protocol appears to output only like 90k strands (maximum) per chip (and that's assuming 100% well...
Forum: Helicos / Direct Genomics 11-22-2010, 12:08 PM
Replies: 18
Views: 14,314
Posted By Lee Sam
They got delisted because their stock price...

They got delisted because their stock price didn't have a price level over $1 per NASDAQ rules.

I have experience with Helicos mRNA-Seq (having just submitted a paper using the technology).
Forum: Illumina/Solexa 11-22-2010, 09:07 AM
Replies: 9
Views: 4,952
Posted By Lee Sam
6% is kind of surprisingly low. We're seeing 20%...

6% is kind of surprisingly low. We're seeing 20% on our transcriptome runs with Bowtie, but I suspect that may have something to do with the library construction and how the paired reads may overlap...
Forum: RNA Sequencing 11-17-2010, 08:30 PM
Replies: 23
Views: 10,143
Posted By Lee Sam
Sorry, I meant that programs running on the head...

Sorry, I meant that programs running on the head nodes themselves (only small 8p servers) can't exceed 15min. Thanks for the advice on rsync.
Forum: RNA Sequencing 11-17-2010, 08:18 PM
Replies: 23
Views: 10,143
Posted By Lee Sam
Red face Thanks for the replies. It sounds like the...

Thanks for the replies. It sounds like the Lawrencium is set up almost exactly like our flux cluster here at UMich. The only issue that we have is that our head nodes don't have our data drives...
Forum: RNA Sequencing 11-17-2010, 12:00 PM
Replies: 23
Views: 10,143
Posted By Lee Sam
We're trying to get the heavy lifting...

We're trying to get the heavy lifting (preprocessing, alignment) parts of ALEXA going on our cluster which uses the Torque scheduler. I know that ALEXA was designed to run on a cluster, was there a...
Forum: Illumina/Solexa 11-08-2010, 08:02 AM
Replies: 9
Views: 4,952
Posted By Lee Sam
HiSeq 2000 RNA-Seq Mapping Rates

We're running and mapping human samples on our new(ish) HiSeq2000 and we're seeing some low mapping rates out of ELAND. Even if you don't run ELAND, I'd be interested in hearing what other HiSeq...
Forum: Bioinformatics 10-25-2010, 12:51 PM
Replies: 30
Views: 10,599
Posted By Lee Sam
Thanks, this is really helpful. I'm working with...

Thanks, this is really helpful. I'm working with dindel too and I was just today wondering about these.
Forum: RNA Sequencing 10-19-2010, 01:47 PM
Replies: 29
Views: 13,448
Posted By Lee Sam
I have a few dozen lanes to run (PE 2x50 GA2...

I have a few dozen lanes to run (PE 2x50 GA2 runs). I suppose I can set it up to run on a cluster I have access to. My experiences have mostly been with SAW (published by some people I know),...
Forum: RNA Sequencing 10-19-2010, 01:23 PM
Replies: 29
Views: 13,448
Posted By Lee Sam
I've been playing with splice discovery tools for...

I've been playing with splice discovery tools for a while. How does the tool perform time-wise? I can't get supersplat to finish, for example.
Forum: RNA Sequencing 10-14-2010, 08:24 PM
Replies: 23
Views: 10,143
Posted By Lee Sam
I figured out my issue. Now I have another...

I figured out my issue. Now I have another question: have you processed any HiSeq data with the pipeline? I started a couple HiSeq lanes 4 hours ago and it isn't even done with the read...
Forum: RNA Sequencing 10-14-2010, 09:36 AM
Replies: 23
Views: 10,143
Posted By Lee Sam
I'm playing with the ALEXA-Seq image, and I'm...

I'm playing with the ALEXA-Seq image, and I'm wondering what kind of data path the scripts require. I ask because I just point it at a common folder /home/alexa-seq/seq_files with .fastq files named...
Forum: Bioinformatics 09-27-2010, 08:51 AM
Replies: 4
Views: 3,052
Posted By Lee Sam
For indel and SV analysis a large number of tools...

For indel and SV analysis a large number of tools are becoming available. However, certain tools are optimized for certain SV sizes (e.g. samtools for indels > ~20bp, breakdancer for SVs > 100bp). I...
Forum: Illumina/Solexa 09-27-2010, 08:47 AM
Replies: 17
Views: 7,076
Posted By Lee Sam
We've seen a similarly huge increase in the...

We've seen a similarly huge increase in the processing times. My personal experience: aligning ~180-200 million 2x100PE whole-genome low coverage data reads from single lanes with BWA from...
Forum: General 09-27-2010, 08:42 AM
Replies: 2
Views: 2,107
Posted By Lee Sam
Hi Joanne. How about trying to align to both...

Hi Joanne. How about trying to align to both exons and splice junctions using short seeds and fairly tight thresholds (20mer, 1 mismatch)? You might end up with some reads that align as both small...
Forum: Bioinformatics 09-22-2010, 01:38 PM
Replies: 5
Views: 6,134
Posted By Lee Sam
Thanks for posting.

Thanks for posting.
Forum: Bioinformatics 09-03-2010, 09:57 AM
Replies: 13
Views: 16,430
Posted By Lee Sam
Thanks for contributing this! It's literally...

Thanks for contributing this! It's literally exactly what I need.
Forum: Literature Watch 08-30-2010, 03:05 PM
Replies: 0
Views: 3,468
Posted By Lee Sam
The genome of the domesticated apple (Malus domestica Borkh.)

The genome of the domesticated apple (Malus domestica Borkh.)

Riccardo Velasco, Andrey Zharkikh, Jason Affourtit, Amit Dhingra, Alessandro Cestaro, Ananth Kalyanaraman, Paolo Fontana, Satish K...
Forum: Bioinformatics 08-27-2010, 02:37 PM
Replies: 40
Views: 16,022
Posted By Lee Sam
How did the belief that dindel was the best indel...

How did the belief that dindel was the best indel caller came about? I haven't seen any comparison papers (at the least I am not aware of them) so I would honestly like to know.
Forum: De novo discovery 08-27-2010, 02:03 PM
Replies: 7
Views: 9,417
Posted By Lee Sam
Here's a page with the link for the DSN...

Here's a page with the link for the DSN normalization protocol. I can't comment further because I honestly don't remember the specifics.

http://www.illumina.com/applications/sequencing/rna.ilmn
Forum: Bioinformatics 08-27-2010, 01:58 PM
Replies: 8
Views: 3,797
Posted By Lee Sam
There is also the consideration that (to my...

There is also the consideration that (to my admittedly shallow understanding) TopHat only uses the set of canonical splice signal sequences. Unfortunately, I can't recommend anything better - I was...
Forum: Bioinformatics 08-27-2010, 01:56 PM
Replies: 40
Views: 16,022
Posted By Lee Sam
I'm running both samtools and GATK as well for...

I'm running both samtools and GATK as well for our exome-captured data. I'm curious why you would consider samtools-exclusive indels as false positives.
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