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Forum: Genomic Resequencing 11-25-2015, 07:21 AM
Replies: 0
Views: 2,822
Posted By chrisbala
psmc bootstrap

Hi All,

I'm messing around with PSMC a bit.

I'm having trouble getting the bootstrap part to run properly. I'm sort of wondering if bwa/samtools updates are causing some issues.

The program...
Forum: RNA Sequencing 10-04-2015, 09:48 AM
Replies: 1
Views: 1,421
Posted By chrisbala
Discriminant Function RNAseq

Following up on this post, has anyone done something like this?

I'm envisioning taking transformed data from say DE-Seq2, and conducting discriminant analysis.

Anyone have experience coding...
Forum: Bioinformatics 06-22-2015, 07:41 AM
Replies: 4
Views: 2,685
Posted By chrisbala
Allelic Depth

Excellent! I'll give it a shot!
Forum: Bioinformatics 06-17-2015, 06:26 AM
Replies: 4
Views: 2,685
Posted By chrisbala
OOps, I meant "bcftools call" not...

OOps, I meant "bcftools call" not vcftools
Forum: Bioinformatics 06-17-2015, 05:15 AM
Replies: 4
Views: 2,685
Posted By chrisbala
Allelic Depth from VCF

I'm trying to estimate the # of reads representing each allele across multiple samples in RNA-seq data.

I've identified SNPs with samtools mpileup and vcftools call, but allelic depth is not...
Forum: General 01-03-2014, 07:20 AM
Replies: 11
Views: 7,483
Posted By chrisbala
thanks!

Got it...

had bowtie2 in two places

/usr/local/bin

and

/usr/local/bin/bowtie2.2blahblah/
Forum: General 01-03-2014, 07:05 AM
Replies: 11
Views: 7,483
Posted By chrisbala
me too

same problem here... bowtie2 runs fine if I am running tophat, but if I try to run bowtie2 directly, I am having the same issue.
Forum: Illumina/Solexa 06-18-2013, 10:45 AM
Replies: 4
Views: 1,541
Posted By chrisbala
offline basecaller

not sure, thanks for the suggestion. i will investigate. I don't know anything about that. usually when I get the data it is already processed!
Forum: Illumina/Solexa 06-18-2013, 07:49 AM
Replies: 4
Views: 1,541
Posted By chrisbala
Illumina pipeline 1.6

Does anyone out there still have access to Cassava 1.6 (or 1.5 or 1.4). Due to a strange set of circumstances, a collaborator of mine has some old data that needs to be re-analyzed from raw images....
Forum: Bioinformatics 05-23-2013, 08:20 AM
Replies: 12
Views: 9,446
Posted By chrisbala
thanks, option 1 is basically what we are doing....

thanks, option 1 is basically what we are doing. but also trying to scrutinize the data in as many ways as possible. we pooled 10 individuals per library, and our results seem not hopeless in that...
Forum: Bioinformatics 05-23-2013, 06:12 AM
Replies: 12
Views: 9,446
Posted By chrisbala
edgeR without replicates

Knowing that it is unwise to do experiments without replication, I find myself in exactly that situation. (pooled samples).

I've analysed these data with older versions of DE-Seq, but now would...
Forum: RNA Sequencing 03-06-2013, 03:56 PM
Replies: 3
Views: 1,929
Posted By chrisbala
Thanks, thats what I'm thinking. I've had...

Thanks, thats what I'm thinking. I've had problems in the past, but that was when a number of things varied on the provider side. Barring that, perhaps its ok..let's see if anyone else has thoughts.
Forum: RNA Sequencing 03-06-2013, 10:12 AM
Replies: 3
Views: 1,929
Posted By chrisbala
library prep batch effects

Hi Everyone,

Do any of you have a sense of how often (or how badly) you see batch effects of library prep and/or sequencing in RNA-seq data (Illumina Tru-Seq kits) ?

Say I've done an...
Forum: RNA Sequencing 02-03-2013, 01:04 PM
Replies: 1
Views: 1,204
Posted By chrisbala
Is it bad form to rekindle an old, unanswered...

Is it bad form to rekindle an old, unanswered thread?

I'm still curious about how Trinity (and other transcriptome assembly software) handles sequence polymorphism in the RNAseq data.

One way...
Forum: RNA Sequencing 12-12-2012, 08:28 AM
Replies: 1
Views: 1,204
Posted By chrisbala
impact of polymorphism on assembly

Hi everyone,

Has anyone assessed the influence of polymorphism (within species) on transcriptome assembly? I have not stumbled upon anything yet.

For example, assembling transcriptomes using...
Forum: Bioinformatics 09-14-2011, 02:16 PM
Replies: 19
Views: 12,705
Posted By chrisbala
has anyone seen any discussion of the influence...

has anyone seen any discussion of the influence of intronic reads on transcript prediction? Or I suppose, mention of how people are dealing with this? I've raised this issue elsewhere and continue to...
Forum: Bioinformatics 07-21-2011, 02:24 PM
Replies: 2
Views: 2,249
Posted By chrisbala
Vsd

Hi Simon,

I just emailed you my commands. Let me know if you need further info.

Thanks!
Forum: Bioinformatics 07-21-2011, 07:52 AM
Replies: 2
Views: 2,249
Posted By chrisbala
DESeq getVarianceStabilizedData

Hi everyone,

I'm using DEseq (Developmental version) on MAC OSX.

I'm trying to use the getVarianceStabilizedData function and am getting an error:

Error in getVarianceStabilizedData(cds) : ...
Forum: Bioinformatics 07-12-2011, 02:40 PM
Replies: 13
Views: 6,008
Posted By chrisbala
devel version

found the relevant thread about needing to install the development version of R as well... done.. things working for noW!
Forum: Bioinformatics 07-12-2011, 12:44 PM
Replies: 13
Views: 6,008
Posted By chrisbala
Ok, last one, it seems something is wrong with...

Ok, last one, it seems something is wrong with the files linked in bioconductor:
http://bioconductor.org/packages/devel/bioc/html/DESeq.html

Am I wrong?
Forum: Bioinformatics 07-12-2011, 11:45 AM
Replies: 13
Views: 6,008
Posted By chrisbala
oops, I think I am just struggling with how to...

oops, I think I am just struggling with how to update DEseq. I am still at DESeq 1.4 and the "update" window is not doing anything...
Forum: Bioinformatics 07-12-2011, 10:19 AM
Replies: 13
Views: 6,008
Posted By chrisbala
Error: could not find function "estimateDispersion"

I'm getting:

Error: could not find function "estimateDispersion"

What have I done wrong?

I'm running R in OSX. I've had no trouble using DEseq before, just this new function.

As far as I...
Forum: De novo discovery 04-20-2011, 08:39 AM
Replies: 58
Views: 46,333
Posted By chrisbala
answer received: I got some output after a few...

answer received: I got some output after a few minutes. Looks like things are going...
Forum: De novo discovery 04-20-2011, 08:24 AM
Replies: 58
Views: 46,333
Posted By chrisbala
Hi everyone, I'm using OASES for the first...

Hi everyone,

I'm using OASES for the first time.

Quick question:
Should I expect anything to be printed to output while OASES is running? (aka immediately after I start the program)

It...
Forum: RNA Sequencing 02-09-2011, 05:58 AM
Replies: 28
Views: 12,623
Posted By chrisbala
I think this issue of excessive cufflinks...

I think this issue of excessive cufflinks predicted transcripts is one many people are wrestling with. I have not figured out a satisfactory way to deal with this other than just using ONLY existing...
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