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Forum: RNA Sequencing 08-02-2017, 09:06 AM
Replies: 11
Views: 3,102
Posted By Richard Barker
They have the HTprocess and Kalisto if you're in...

They have the HTprocess and Kalisto if you're in a rush
Forum: RNA Sequencing 08-02-2017, 08:52 AM
Replies: 11
Views: 3,102
Posted By Richard Barker
I used the pipeline that was made in the CyVerse...

I used the pipeline that was made in the CyVerse Discovery environment. It's easy to use and really fast!
Forum: Service Providers 07-22-2013, 09:12 AM
Replies: 13
Views: 9,127
Posted By Richard Barker
Dear Narain I totally agree. I spent/wasted a...

Dear Narain
I totally agree. I spent/wasted a lot of time setting up a virtual unix machine and install tools and their various dependencies. Hence i was so pleased when i found the iPlant team had...
Forum: Service Providers 07-22-2013, 06:25 AM
Replies: 13
Views: 9,127
Posted By Richard Barker
Hi Narain, did you read the previous thread? I'm...

Hi Narain, did you read the previous thread? I'm not sure your post is appropirate as this thread is about sequencing companies and not a place to advertise private companies that do sequence...
Forum: RNA Sequencing 07-15-2013, 06:38 AM
Replies: 4
Views: 1,753
Posted By Richard Barker
Dear Heather I didn't solve that issue in...

Dear Heather

I didn't solve that issue in the end so found a couple of ways around the issue. The first thing i did was set up a free account with the iPlant collaborative...
Forum: Bioinformatics 02-05-2013, 07:36 PM
Replies: 3
Views: 1,510
Posted By Richard Barker
I'm also to trying to generate a VCF (to use to...

I'm also to trying to generate a VCF (to use to generate counts per gene with some Arabidopsis RNAseq data i have) file for Arabidopsis thaliana but am not sure where to start... any advice
Forum: Bioinformatics 01-10-2013, 05:44 AM
Replies: 5
Views: 901
Posted By Richard Barker
Wow, thats a lot of replicates, so your initial...

Wow, thats a lot of replicates, so your initial table has 120 columns? And in the first row 44 of them just have A, 23 have B and 55 are C?
I've heard of an experiment with so many rep's before so...
Forum: Bioinformatics 01-10-2013, 05:36 AM
Replies: 5
Views: 901
Posted By Richard Barker
Could you explain what the numbers and letters...

Could you explain what the numbers and letters refer to in the following line?

condition = factor(c(rep("A", 44), rep("B", 21), rep("C", 55)))

I
Forum: RNA Sequencing 01-10-2013, 05:31 AM
Replies: 4
Views: 2,049
Posted By Richard Barker
Hi dpyan Can you share the commands that you...

Hi dpyan
Can you share the commands that you used for DESeq so i can see a functional example to try and guide my future attempts?
Forum: RNA Sequencing 01-09-2013, 02:58 PM
Replies: 4
Views: 862
Posted By Richard Barker
Ooops, i see... I used the University of...

Ooops, i see...
I used the University of Wisconsin's biotechnilogy center, they had a fast turn around and produced high quality data...
http://www.biotech.wisc.edu/facilities/dnaseq/home
Forum: Bioinformatics 01-09-2013, 02:54 PM
Replies: 5
Views: 901
Posted By Richard Barker
Can you share the code/script you used as it...

Can you share the code/script you used as it might make the issue a bit clearer?
Forum: Service Providers 01-09-2013, 02:53 PM
Replies: 13
Views: 9,127
Posted By Richard Barker
I had all my sequencing donw at the University of...

I had all my sequencing donw at the University of Wisconsin's biotechnology center. It was quick and i received very high quality data.

http://www.biotech.wisc.edu/facilities/dnaseq/home
Forum: RNA Sequencing 01-09-2013, 02:48 PM
Replies: 4
Views: 2,049
Posted By Richard Barker
For cuffdiff i normally use 10 as the minimum...

For cuffdiff i normally use 10 as the minimum per-locus counts for significance testing. Hope this helps... I'm now trying to get DESeq working so can't help with that one...
Forum: RNA Sequencing 01-09-2013, 02:45 PM
Replies: 4
Views: 862
Posted By Richard Barker
I recormend the iPlant cyberinfrastruture for...

I recormend the iPlant cyberinfrastruture for analysis. They have the Tuxedo2 protocol intergrated into a user friendly graphical interface that links to some supercomputer clusters in Arazona and...
Forum: Bioinformatics 12-11-2012, 11:35 AM
Replies: 7
Views: 1,457
Posted By Richard Barker
The latest version is being installed on iPlant...

The latest version is being installed on iPlant this week so i lookforward to using it...
Forum: Bioinformatics 12-03-2012, 09:17 PM
Replies: 7
Views: 1,457
Posted By Richard Barker
The original SAM file was generated with...

The original SAM file was generated with tophat2and bowtie2 using the following command.

[user]$ tophat -o output_name_bowtie2_for_splicegrapher --no-convert-bam -a 10 -g 1 -F 0 -p 6...
Forum: Bioinformatics 12-03-2012, 03:31 PM
Replies: 7
Views: 1,457
Posted By Richard Barker
hello I'm also having issues with splicegrapher...

hello
I'm also having issues with splicegrapher but at the next stage. So gene_model_to_splicegraph.py has split my custom GFF into chromosomes and the sam_collate.py command has split my sample.sam...
Forum: RNA Sequencing 12-03-2012, 10:30 AM
Replies: 4
Views: 1,753
Posted By Richard Barker
Error in CummeRbund while creating database

Hello

I'm trying to investigate my Tophat 2.05 Bowtie 2.0 aligned BAM file, plus BAM bai file and cuffdiff 2.02 outputs using the latest version of cummeRbund in R version 2.15.2.

While...
Forum: RNA Sequencing 10-30-2012, 01:54 PM
Replies: 6
Views: 2,833
Posted By Richard Barker
So would you recommend that we/i normalize my...

So would you recommend that we/i normalize my data by the upper quartile of the number of fragments mapping to individual loci when running cufflinks? or should one just omit this option?
Forum: RNA Sequencing 10-30-2012, 01:39 PM
Replies: 8
Views: 7,462
Posted By Richard Barker
I'm not sure whats wrong but you could try a...

I'm not sure whats wrong but you could try a different approach... I personally use the iPlant collaborative cloud infrastructure http://www.iplantcollaborative.org/...

Simple go to their website...
Forum: RNA Sequencing 10-24-2012, 08:37 AM
Replies: 2
Views: 2,649
Posted By Richard Barker
You can analyze your files separately and then...

You can analyze your files separately and then merge your repeats during the cuffdiff stage, the iplant website has a really user friendly tutorial and the iplant collaborative cloud infrastructure...
Forum: RNA Sequencing 10-09-2012, 08:51 AM
Replies: 7
Views: 1,548
Posted By Richard Barker
Hello You could use the iplant collaborative...

Hello
You could use the iplant collaborative infrastructure... Setup an account, upload your data to the data store and then use their cloud infrastructure to run your alignment on their super...
Forum: Bioinformatics 09-27-2012, 01:37 PM
Replies: 6
Views: 3,223
Posted By Richard Barker
I'm having the same problem. I have RNAseq data...

I'm having the same problem. I have RNAseq data that i analysed using the Tuxedo protocol. If i use the custom GTF file generated by cufflinks/cuffmerge then i can see there are lots of new splice...
Forum: Bioinformatics 09-27-2012, 01:26 PM
Replies: 6
Views: 3,001
Posted By Richard Barker
Can i also vote for a PCA component for...

Can i also vote for a PCA component for cummeRbund? :)
Forum: RNA Sequencing 09-27-2012, 01:22 PM
Replies: 2
Views: 1,809
Posted By Richard Barker
you could try the iplant system

If you use the TopHat GUI based application within the iplant discovery environment (http://www.iplantcollaborative.org/discover/discovery-environment) then it automatically produces a BAM file with...
Showing results 1 to 25 of 47

 


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