Header Leaderboard Ad

Collapse

How to name samples in CummeRbund?

Collapse

Announcement

Collapse

SEQanswers June Challenge Has Begun!

The competition has begun! We're giving away a $50 Amazon gift card to the member who answers the most questions on our site during the month. We want to encourage our community members to share their knowledge and help each other out by answering questions related to sequencing technologies, genomics, and bioinformatics. The competition is open to all members of the site, and the winner will be announced at the beginning of July. Best of luck!

For a list of the official rules, visit (https://www.seqanswers.com/forum/sit...wledge-and-win)
See more
See less
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • How to name samples in CummeRbund?

    Hello,

    Problem: I cannot figure out which sample is which in Cummerbund or how to name them.

    Details:
    I used Galaxy to run Cufflinks, Cuffmerge, and Cuffdiff. I then downloaded files, renamed them to Cufflinks convention and am trying to visualize my data with CummeRbund in RStudio. I cannot figure out which sample is which and how to name them. For example, my density plot just shows samples as q1, q2.

    Can someone please help me out?

  • #2
    It seems possible that the only way to do this is to rename sample names from Sample1/q1, Sample2/q2, etc. in cuffdiff output. I understand from Cufflinks manual that the first sample input into cuffdiff is Sample1/q1 and the second is Sample2/q2.

    For example,

    285: control.bam
    287: test.bam
    414: cuffmerge.gtf

    425: Cuffdiff on data 285, data 287, and data 414: transcript FPKM tracking

    Output
    Sample 1= q1 = 285 = control.bam
    Sample 2 = q2 = 287 = test. bam

    Can someone confirm this and touch on whether this is normal workflow? Is there a way to enable Galaxy to keep original sample names?
    Last edited by veber; 05-25-2012, 04:40 PM.

    Comment


    • #3
      *Bump

      Anyone?

      Comment


      • #4
        N.B. I'm not familiar with Galaxy. Cuffdiff will set q1/q2 in the order of the files given to it. That is, if you execute "cuffdiff OPTIONS transcripts.gtf control.bam test.bam" or similar then control is usually q1. In the future, use the "-L Label1,Label2,..." switch to make your life easier. I would assume there's a way to do that in Galaxy.

        Comment


        • #5
          sed replacment

          If you run the experiment with several samples

          ie. cuffdiff -o cuffdiff/all REF.gff SAMPLE1.bam,SAMPLE1a.bam,SAMPLE1b.bam SAMPLE2.bam,SAMPLE2a.bam,SAMPLE2b.bam SAMPLE3.bam,SAMPLE3a.bam,SAMPLE3b.bam

          you can rename them by entering cuffdiff output directory and running:

          sed -i.bak -e 's/q1/SAMPLE1/g;s/q2/SAMPLE2/g;s/q3/SAMPLE3/g' *.diff *.info *_tracking

          Comment

          Latest Articles

          Collapse

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, Yesterday, 10:20 AM
          0 responses
          9 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 06-07-2023, 07:14 AM
          0 responses
          13 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 06-06-2023, 01:08 PM
          0 responses
          13 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 06-01-2023, 08:56 PM
          0 responses
          166 views
          0 likes
          Last Post seqadmin  
          Working...
          X