Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Galaxy -> cummeRbund How? ekimmike Bioinformatics 5 07-25-2019 06:03 AM
Cufflinks settings on Galaxy mshamblott Bioinformatics 0 05-18-2013 04:40 PM
Data from Galaxy CuffDiff to cummeRbund reb_chen Bioinformatics 0 02-12-2013 03:37 PM
cufflinks cummeRbund set condition Jetse Bioinformatics 1 12-11-2012 05:48 AM
Cufflinks error via Galaxy puggie Bioinformatics 0 03-23-2012 05:07 AM

Thread Tools
Old 04-02-2014, 09:57 AM   #1
Location: Kansas City

Join Date: Jan 2014
Posts: 18
Question Galaxy Cufflinks -> cummeRbund?


I found a useful thread here that is related to what I am doing, but not quite. Galaxy may be missing some files I need? I don't know. Here is what I want to do.

1. Read in cuffSet object using readCufflinks()
cuffData = readCufflinks("data")

2. Once I have this cuffData, I want to draw a volcano plot as follows
sigGene = csVolcano(genes(cuffData), "treatment1", "treatment2")

That's it.

My problems are as follows:
1. See my attached files. I need to save galaxy output to be recognized by readCufflinks(). However, see my error message. I am going to need all the default files readCufflinks requires. But I don't see where galaxy saved isoforms.fpkm_tracking. I just don't see it? Is it transcript FPKM tracking?

2. If all I want is to make a volcano plot as mentioned in 2. Can I just load the gene diff and fpkm tracking file for readCufflinks? Or do I need all the output from galaxy?

3. Right now I am manually saving the output files and renaming them, but is there a better way to output galaxy cufflink output?
Attached Images
File Type: png Screenshot from 2014-04-02 11:46:05.png (88.8 KB, 7 views)
File Type: png Screenshot from 2014-04-02 11:50:23.png (48.8 KB, 4 views)
hyates is offline   Reply With Quote
Old 04-02-2014, 10:43 AM   #2
Location: Kansas City

Join Date: Jan 2014
Posts: 18

I think I may have found the solution here. However, before I can claim this is solved, can I have some folks in the community confirm some things for me? For example, that transcript differention expression from galaxy output is actually isoform.diff and so on? Why would they name files different like this from cuffdiff output defaults? I am just trying to figure out what is galaxy calling an output and what cummeRbund thinks it is. I am, I think, super close.
hyates is offline   Reply With Quote

cummerbund, galaxy, r language, rna-seq beginner

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 05:46 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO