Forum: Bioinformatics
06-07-2017, 11:44 AM
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Replies: 6
Views: 2,124
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Forum: Bioinformatics
06-07-2017, 10:43 AM
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Replies: 6
Views: 2,124
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Forum: Bioinformatics
06-07-2017, 06:10 AM
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Replies: 6
Views: 2,124
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Forum: Bioinformatics
06-06-2017, 06:47 PM
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Replies: 6
Views: 2,124
bowtie2-build python error
Hi
We installed bowtie2-2.3.2 on an ubuntu system.
Running bowtie2-build we received the following error that I think indicates problems with the python installation??
./bowtie2-build...
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Forum: Bioinformatics
05-05-2015, 07:02 PM
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Replies: 1
Views: 1,154
DESeq2 experimental design/analysis
Nieve statistical question
We have the following data:
control: 3 biological replicates
treatment 1: 2 biological replicates
treatment 2: 2 biological replicates
Using DESeq2 and running 3...
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Forum: Bioinformatics
04-18-2015, 05:14 AM
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Replies: 0
Views: 809
parse GFF3 longest mRNA
Hi
Interested in editing a gff3 file so that it contains only the longest mRNAs, and corresponding gene,exons, CDS, UTRs.
Looking at BioPerl, I don't see a method for accessing the 'attributes'...
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Forum: Bioinformatics
10-23-2014, 08:51 AM
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Replies: 0
Views: 1,192
seqmonk - java memory error
Hi
I have seqmonk installed on a linux system
$ java -version
java version "1.7.0_65"
OpenJDK Runtime Environment (IcedTea 2.5.1) (7u65-2.5.1-4ubuntu1~0.14.04.2)
OpenJDK 64-Bit Server VM...
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Forum: Bioinformatics
09-09-2014, 09:26 AM
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Replies: 2
Views: 996
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Forum: Bioinformatics
09-09-2014, 07:59 AM
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Replies: 2
Views: 996
Illumina reads- noise in 1st 12nt
Hi
We have Illumina paired end reads, and when we look at them w/ TrimGalore we see the the anomaly in the 1st 12-13 bases in the sequence content plot.
Are these adapters, and should they be...
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Forum: Bioinformatics
07-04-2014, 11:45 AM
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Replies: 0
Views: 1,361
tophat: Indexing splices
Hi
I received the error below when running tophat with some old reads (35nt).
the file, bowtie-build is references as a symlink in .../bin (bowtie2-build ->...
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Forum: Bioinformatics
06-19-2014, 06:53 PM
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Replies: 0
Views: 1,536
cuffdiff- no assembled transcripts
Hi
We are running tophat pipeline on algal sequences and our cuffdiff output does not appear to have assembled transcripts listed, rather CDS that correlate w/ single exons only.
tophat:...
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Forum: Bioinformatics
04-24-2014, 02:48 PM
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Replies: 2
Views: 1,464
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Forum: Bioinformatics
04-23-2014, 07:38 PM
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Replies: 2
Views: 1,464
mapping RNASeq w/ tophat: 3'UTR enrichment
Hi
I have 2 sets of Illumina rnaseq reads that were mapped using tophat.
Each set of reads was prepped/sequenced by different labs
1 set is recent (paired-end)
1 set is old (35nt single end)
...
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Forum: General
09-23-2013, 03:36 PM
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Replies: 0
Views: 1,386
RNASeq experimental design
All
Hope I can pick your collective wisdom/experience.
A collaborator is planning to carry out an RNASeq experiment and separately, a RIPSeq experiment, and is looking for guidance regarding...
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Forum: Bioinformatics
06-25-2012, 01:08 PM
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Replies: 0
Views: 1,417
cuffdiff log2(FC) when 1 condition has 0 counts
Hi
Working our way thru the cuffdiff output and see that when one condition has 0 counts cuffdiff must utilize a fudge factor and reports a value of -1.79769e+308.
In most cases where the other...
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Forum: Bioinformatics
06-07-2012, 07:25 AM
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Replies: 2
Views: 2,431
cuffmerge - error reading ref.gtf
Hi
Attempted to run cuffmerge and received the following error:
You are using Cufflinks v2.0.0, which is the most recent release.
Error: duplicate GFF ID 'Cre01.g000050.t1.2' encountered!...
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Forum: Bioinformatics
04-08-2012, 01:50 PM
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Replies: 4
Views: 7,709
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Forum: Bioinformatics
04-05-2012, 07:28 PM
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Replies: 4
Views: 7,709
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Forum: Bioinformatics
01-04-2012, 07:25 AM
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Replies: 7
Views: 13,122
bowtie memory warning
All
Thanks for the advice:
Using --chunkmbs 200 eliminated the memory warnings.
I'm still not mapping a significant fraction of the reads. I'm going to trim the unmapped colorspace reads...
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Forum: Bioinformatics
01-03-2012, 11:48 AM
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Replies: 7
Views: 13,122
bowtie memory warning
Hi
I'm mapping solid reads using bowtie and received the following warnings for MANY reads. Mapping % is very low as well.
Am I running out of memory?
command line:
bowtie -C -S -k 3 --best...
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Forum: Bioinformatics
12-31-2011, 10:29 AM
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Replies: 0
Views: 1,080
Extracting 'counts' from v values
All,
We were given a data set of Solid reads mapped. The values are reported as 'v values': nt/length/reads. I'd like to extract raw counts from the data for use with DESeq.
I think I...
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Forum: Bioinformatics
12-31-2011, 10:24 AM
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Replies: 1
Views: 3,053
DESeq: problem updating to new version
Hi All,
I attempted to upgrade DESeq to the new version and received an error that I was missing library 'xtable'.
I checked cran and the link to xtable is dead.
This is on a Mac 10.6.8...
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Forum: Bioinformatics
12-22-2011, 12:44 PM
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Replies: 43
Views: 27,438
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Forum: Bioinformatics
12-22-2011, 09:12 AM
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Replies: 43
Views: 27,438
DESeq w/o replicates - padj
Hi New to RNASeq.
We are looking at data w/o replicates (bad I know, but $$ prohibited).
Can someone explain how I interpret padj values =1. I believe this is a measure of FDR type I error?
...
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Forum: Bioinformatics
08-09-2011, 03:15 PM
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Replies: 6
Views: 2,004
Hi All,
I've checked the # reads mapping to...
Hi All,
I've checked the # reads mapping to 5utr, cds,3utr and it does appear there was likely degradation of the polyA prior to fragmentation:
>summary(cds$utr5)
Min. 1st Qu. Median ...
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