Forum: Genomic Resequencing
11-25-2015, 07:21 AM
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Replies: 0
Views: 3,093
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...
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Forum: RNA Sequencing
10-04-2015, 09:48 AM
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Replies: 1
Views: 1,590
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...
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Forum: Bioinformatics
06-22-2015, 07:41 AM
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Replies: 4
Views: 3,060
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Forum: Bioinformatics
06-17-2015, 06:26 AM
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Replies: 4
Views: 3,060
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Forum: Bioinformatics
06-17-2015, 05:15 AM
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Replies: 4
Views: 3,060
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...
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Forum: General
01-03-2014, 07:20 AM
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Replies: 11
Views: 7,864
thanks!
Got it...
had bowtie2 in two places
/usr/local/bin
and
/usr/local/bin/bowtie2.2blahblah/
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Forum: General
01-03-2014, 07:05 AM
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Replies: 11
Views: 7,864
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.
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Forum: Illumina/Solexa
06-18-2013, 10:45 AM
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Replies: 4
Views: 1,654
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!
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Forum: Illumina/Solexa
06-18-2013, 07:49 AM
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Replies: 4
Views: 1,654
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....
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Forum: Bioinformatics
05-23-2013, 08:20 AM
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Replies: 12
Views: 10,387
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Forum: Bioinformatics
05-23-2013, 06:12 AM
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Replies: 12
Views: 10,387
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...
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Forum: RNA Sequencing
03-06-2013, 03:56 PM
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Replies: 3
Views: 2,158
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.
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Forum: RNA Sequencing
03-06-2013, 10:12 AM
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Replies: 3
Views: 2,158
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...
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Forum: RNA Sequencing
02-03-2013, 01:04 PM
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Replies: 1
Views: 1,337
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...
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Forum: RNA Sequencing
12-12-2012, 08:28 AM
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Replies: 1
Views: 1,337
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...
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Forum: Bioinformatics
09-14-2011, 02:16 PM
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Replies: 19
Views: 13,601
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...
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Forum: Bioinformatics
07-21-2011, 02:24 PM
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Replies: 2
Views: 2,425
Vsd
Hi Simon,
I just emailed you my commands. Let me know if you need further info.
Thanks!
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Forum: Bioinformatics
07-21-2011, 07:52 AM
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Replies: 2
Views: 2,425
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) : ...
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Forum: Bioinformatics
07-12-2011, 02:40 PM
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Replies: 13
Views: 6,361
devel version
found the relevant thread about needing to install the development version of R as well... done.. things working for noW!
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Forum: Bioinformatics
07-12-2011, 12:44 PM
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Replies: 13
Views: 6,361
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Forum: Bioinformatics
07-12-2011, 11:45 AM
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Replies: 13
Views: 6,361
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Forum: Bioinformatics
07-12-2011, 10:19 AM
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Replies: 13
Views: 6,361
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Forum: De novo discovery
04-20-2011, 08:39 AM
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Replies: 58
Views: 51,173
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Forum: De novo discovery
04-20-2011, 08:24 AM
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Replies: 58
Views: 51,173
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...
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Forum: RNA Sequencing
02-09-2011, 05:58 AM
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Replies: 28
Views: 13,376
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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