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Forum: Bioinformatics 06-07-2017, 10:44 AM
Replies: 6
Views: 1,657
Posted By crh
Alec Moving the python3.4 info into PATH and...

Alec

Moving the python3.4 info into PATH and out of PYTHONPATH solved the problem.

Thanks!
Forum: Bioinformatics 06-07-2017, 09:43 AM
Replies: 6
Views: 1,657
Posted By crh
Here is what /env is set to: ...

Here is what /env is set to:

charlesh@~/binf/src/bowtie2-2.3.2 => /usr/bin/env python --version
Python 2.7.6

PYTHONPATH...
Forum: Bioinformatics 06-07-2017, 05:10 AM
Replies: 6
Views: 1,657
Posted By crh
Python 3.4.3 and 2.7 are installed on the system....

Python 3.4.3 and 2.7 are installed on the system.

Python 3.4.3 appears to be the default.

charlesh@~/binf/src/bowtie2-2.3.2 => python
Python 3.4.3 (default, Nov 17 2016, 01:08:31)
[GCC...
Forum: Bioinformatics 06-06-2017, 05:47 PM
Replies: 6
Views: 1,657
Posted By crh
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...
Forum: Bioinformatics 05-05-2015, 06:02 PM
Replies: 1
Views: 1,071
Posted By crh
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...
Forum: Bioinformatics 04-18-2015, 04:14 AM
Replies: 0
Views: 746
Posted By crh
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'...
Forum: Bioinformatics 10-23-2014, 07:51 AM
Replies: 0
Views: 1,117
Posted By crh
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...
Forum: Bioinformatics 09-09-2014, 08:26 AM
Replies: 2
Views: 931
Posted By crh
Great - thanks for quick reply Charles

Great - thanks for quick reply

Charles
Forum: Bioinformatics 09-09-2014, 06:59 AM
Replies: 2
Views: 931
Posted By crh
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...
Forum: Bioinformatics 07-04-2014, 10:45 AM
Replies: 0
Views: 1,262
Posted By crh
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 ->...
Forum: Bioinformatics 06-19-2014, 05:53 PM
Replies: 0
Views: 1,456
Posted By crh
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:...
Forum: Bioinformatics 04-24-2014, 01:48 PM
Replies: 2
Views: 1,387
Posted By crh
Thanks for reply. I checked on RNA RIN's, and...

Thanks for reply.
I checked on RNA RIN's, and the samples had RINs between 7.2 and 8.5.

I'll check on the thread supplied.

Charles
Forum: Bioinformatics 04-23-2014, 06:38 PM
Replies: 2
Views: 1,387
Posted By crh
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)
...
Forum: General 09-23-2013, 02:36 PM
Replies: 0
Views: 1,297
Posted By crh
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...
Forum: Bioinformatics 06-25-2012, 12:08 PM
Replies: 0
Views: 1,324
Posted By crh
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...
Forum: Bioinformatics 06-07-2012, 06:25 AM
Replies: 2
Views: 2,303
Posted By crh
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!...
Forum: Bioinformatics 04-08-2012, 12:50 PM
Replies: 4
Views: 7,247
Posted By crh
Correct you are - retyping seems to have fixed...

Correct you are - retyping seems to have fixed the error - thanks!

Charles
Forum: Bioinformatics 04-05-2012, 06:28 PM
Replies: 4
Views: 7,247
Posted By crh
cuffdiff Error: cannot open reference GTF file L for reading

Hi

I ran tophat with replicate samples for a control & treated sample, then ran cufflinks, followed by cuffmerge. I provided a GTF file to cuffmerge.

When I attempt to run cuffdiff I get the...
Forum: Bioinformatics 01-04-2012, 06:25 AM
Replies: 7
Views: 12,690
Posted By crh
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...
Forum: Bioinformatics 01-03-2012, 10:48 AM
Replies: 7
Views: 12,690
Posted By crh
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...
Forum: Bioinformatics 12-31-2011, 09:29 AM
Replies: 0
Views: 1,015
Posted By crh
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...
Forum: Bioinformatics 12-31-2011, 09:24 AM
Replies: 1
Views: 2,918
Posted By crh
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...
Forum: Bioinformatics 12-22-2011, 11:44 AM
Replies: 43
Views: 26,728
Posted By crh
No replicates

Duly noted.

c
Forum: Bioinformatics 12-22-2011, 08:12 AM
Replies: 43
Views: 26,728
Posted By crh
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?
...
Forum: Bioinformatics 08-09-2011, 02:15 PM
Replies: 6
Views: 1,897
Posted By crh
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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