SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 191
Search took 0.02 seconds.
Search: Posts Made By: RockChalkJayhawk
Forum: Events / Conferences 02-10-2014, 06:23 AM
Replies: 4
Views: 1,132
Posted By RockChalkJayhawk
My liver has been conditioning for this...

My liver has been conditioning for this conference all year. :D
Forum: Events / Conferences 02-07-2014, 12:46 PM
Replies: 4
Views: 1,132
Posted By RockChalkJayhawk
Agbt2014

Anyone planning a get together at AGBT? I'm sure we could find some free drinks! :D
Forum: Ion Torrent 12-13-2013, 04:46 AM
Replies: 5
Views: 2,998
Posted By RockChalkJayhawk
Not sure. All I know is that there are several...

Not sure. All I know is that there are several 9-15bp indels that are Sanger validated that are not getting aligned. I know BWA will not usually align reads with indels > 8bp, but Novoalign does. ...
Forum: Ion Torrent 12-09-2013, 09:49 AM
Replies: 5
Views: 2,998
Posted By RockChalkJayhawk
Thanks Torrent!

Thanks Torrent!
Forum: RNA Sequencing 12-06-2013, 09:07 AM
Replies: 3
Views: 1,700
Posted By RockChalkJayhawk
I hadn't actually seen it before, but it is a...

I hadn't actually seen it before, but it is a very good looking web app! The power estimates should be similar, but won't be identical for 2 reasons:

1. Scotty assumes that variance follows a...
Forum: RNA Sequencing 12-06-2013, 08:16 AM
Replies: 3
Views: 1,700
Posted By RockChalkJayhawk
Calculating Sample Size Estimates for RNA Sequencing Data

I know this was picked up by the Newsbot, but I would like to mention that we created an R package on bioconductorthat can calculate sample size, power, effect sizes, etc. The paper is located here...
Forum: Ion Torrent 12-06-2013, 06:59 AM
Replies: 5
Views: 2,998
Posted By RockChalkJayhawk
Primer Sequences for Cancer Panels

Does anyone know what the exact primer sequences are for the cancer panels? I really need to know so I can remove them during the alignment step. Otherwise it causes certain indels to be missed.
Forum: Genomic Resequencing 08-25-2013, 07:13 PM
Replies: 2
Views: 1,123
Posted By RockChalkJayhawk
Seems like your file is not actually valid. You...

Seems like your file is not actually valid. You should have a GT entry in the format field, along with the sample name. If you don't have it, then you should remove the last column altogether.
Forum: Bioinformatics 01-16-2013, 09:02 PM
Replies: 3
Views: 729
Posted By RockChalkJayhawk
Ryan, I wrote SoftSearch and would be happy to...

Ryan,
I wrote SoftSearch and would be happy to help if you're interested. I'm updating the website regularly with improvements, trying to get ready for paper submission, so make sure you use the...
Forum: Bioinformatics 11-02-2012, 10:54 AM
Replies: 0
Views: 500
Posted By RockChalkJayhawk
Visualizing Integrated data

All,
Several papers are coming out now with plots that show the type and frequency of somatic mutaions, CNV, expression, etc. One example is from this paper here...
Forum: Genomic Resequencing 08-14-2012, 07:25 PM
Replies: 2
Views: 1,138
Posted By RockChalkJayhawk
check the fields in the gatk vcf. It already...

check the fields in the gatk vcf. It already tells you how many reference/alternate reads there are.
Forum: Bioinformatics 07-11-2012, 02:07 PM
Replies: 6
Views: 3,508
Posted By RockChalkJayhawk
can you post the error message from GATK?

can you post the error message from GATK?
Forum: Bioinformatics 07-11-2012, 08:03 AM
Replies: 6
Views: 3,508
Posted By RockChalkJayhawk
We've switched to the updated Tophat2, which...

We've switched to the updated Tophat2, which seems to work well.
Forum: Bioinformatics 06-06-2012, 03:35 AM
Replies: 10
Views: 2,177
Posted By RockChalkJayhawk
Any response?

Any response?
Forum: Bioinformatics 04-10-2012, 04:56 AM
Replies: 12
Views: 3,359
Posted By RockChalkJayhawk
@RockChalkJayhawk and others who have used...

@RockChalkJayhawk and others who have used BreakDancer
I'm running some 100GB whole genome Illumina sequencing files on BreakDancer. The program has been running for 2 weeks and has done 500...
Forum: Bioinformatics 03-27-2012, 01:00 PM
Replies: 10
Views: 1,514
Posted By RockChalkJayhawk
The problem is I am using an RNA-Seq workflow...

The problem is I am using an RNA-Seq workflow that produces a pileup rather than a BAM, so I can't annotate it with GATK.
Forum: Bioinformatics 03-27-2012, 10:57 AM
Replies: 10
Views: 1,514
Posted By RockChalkJayhawk
Yes, but theoretically you can re-create the BAM...

Yes, but theoretically you can re-create the BAM information from the pileup because all the information is stored in the pileup file. Or am I mistaken?
Forum: Bioinformatics 03-27-2012, 06:48 AM
Replies: 10
Views: 1,514
Posted By RockChalkJayhawk
pileup2bam

Anyone aware of a tool that can convert a pileup file to BAM files.
Forum: Bioinformatics 03-21-2012, 04:45 AM
Replies: 10
Views: 2,177
Posted By RockChalkJayhawk
I guessed people just made them in powerpoint,...

I guessed people just made them in powerpoint, but if there is such a tool, I'd be very interested.
Forum: Bioinformatics 03-10-2012, 06:20 AM
Replies: 12
Views: 3,359
Posted By RockChalkJayhawk
I usually take a 3-tiered approach, using...

I usually take a 3-tiered approach, using CNVnator (read Depth), Break Dancer (Read pair) and CREST (split read). However, I too see a lot fo false positives from each tool. What would be great is...
Forum: Bioinformatics 03-10-2012, 06:13 AM
Replies: 2
Views: 4,035
Posted By RockChalkJayhawk
SomaticSniper filtering

I too have had this problem with SomaticSniper. I reccomend filtering out those call where 5% of the alternate allele can be found in the normal sample. I would be interested in Someone from Wash U...
Forum: Bioinformatics 02-25-2012, 02:52 PM
Replies: 3
Views: 807
Posted By RockChalkJayhawk
Cufflinks should also report gene expression for...

Cufflinks should also report gene expression for you. Otherwise I would use mergeBed from BEDtools to build a consensus.
Forum: Bioinformatics 02-24-2012, 10:47 AM
Replies: 1
Views: 1,443
Posted By RockChalkJayhawk
from the README The program will...

from the README


The program will generate a *.predSV.txt file. The filename will be the input
bam with .predSV.txt appended unless you specify the -p parameter. Also the
STDERR output has...
Forum: Bioinformatics 02-09-2012, 07:37 AM
Replies: 9
Views: 4,274
Posted By RockChalkJayhawk
Thanks John. Do you know if it uses only the...

Thanks John. Do you know if it uses only the positional information for annotation or the position combined with the type/alternate of variant?
Forum: Bioinformatics 02-09-2012, 05:10 AM
Replies: 9
Views: 4,274
Posted By RockChalkJayhawk
In a developmental tool by GATK, one of the input...

In a developmental tool by GATK, one of the input files is a cosmic vcf see here https://confluence.broadinstitute.org/display/CGATools/MuTect. I just emailed the group to find out where to download...
Showing results 1 to 25 of 191

 


All times are GMT -8. The time now is 07:31 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO