This is a test version of Biostars. For the public version, visit https://www.biostars.org.
readcufflinks shows error in R cummeRbund Package

There are two samples and I have performed the analysis as given in paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3334321/ . But when I performed cummeRbund it gave following output.

cuffl <-readCufflinks('diff_out')

cuffl

CuffSet instance with:

 0 samples
 0 genes
 0 isoforms
 0 TSS
 0 CDS
 0 promoters
 0 splicing
 0 relCDS

The file is attached diff_out

rna-seq software error r cummerbund
• 4,075 views • link
updated by Satyajeet Khare Satyajeet Khare • written by Mask Mask

Are you in the working directory (cuffdiff out folder)? Can you try following?

setwd("/your_cuffdiff_out_directory_location")
cuffl <-readCufflinks()
• 0 views • link
written by Satyajeet Khare Satyajeet Khare

Yes. In working directory only. I have attached the file (diff_out) . The size of the folder is very less. Can you download and perform cummeRbund on that

• 0 views • link
written by Mask Mask

I'm not sure why this thread was deleted after it was answered... reopened.

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted. Upvote|Bookmark|Accept

Welcome to biostars. Interesting guidelines for posting can be found in the following posts:

• 0 views • link
written by WouterDeCoster WouterDeCoster

1 answer

I removed files that were not generated by cuffdiff and got this result...

CuffSet instance with:
     2 samples
     1558 genes
     1947 isoforms
     1658 TSS
     0 CDS
     1558 promoters
     1658 splicing
     0 relCDS

So my suggestion is, dont alter cuffdiff output :)

• 0 views • link
written by Satyajeet Khare Satyajeet Khare

Can you tell me which all files did you remove from the folder? Thank you

• 0 views • link
written by Mask Mask

You will get more help from the community if you up-vote answers to your questions than your own questions and comments.

• 0 views • link
written by Satyajeet Khare Satyajeet Khare

okay... Can you tell me which all files did you remove from the folder?

• 0 views • link
written by Mask Mask

Can someone do that ? up-vote own posts ?

• 0 views • link
written by GouthamAtla GouthamAtla

Looks like you cannot. My bad. Just saw score rising from 0 to 200 in a matter of minutes so grew suspicious. Apologies.

• 0 views • link
written by Satyajeet Khare Satyajeet Khare

It looks suspicious though, 0 to 200, which I had noticed as well.

• 0 views • link
written by GouthamAtla GouthamAtla

It is definitely suspicious. A warning has been issued to @Mask. I will also keep an eye out for future infarctions.

• 0 views • link
written by Ram Ram

Upvote baiting is not good etiquette.

• 0 views • link
written by Ram Ram

Log in to answer this question.

More posts like this
  • Error about using cummeRbund package to load cuffdiff output data
    written by 673422688 • 673422688
    I had analyzed the RNA-seq data with Tophat-Cufflinks-Cuffdiff procedure. when I used the cummeRbund package by R I can not read the diffout data correctly …
  • Getting MDSplot from Cufflinks data [cummeRbund]
    written by anu014 anu014
    Hello Biostars, I am doing MDSplot like this : library(cummeRbund) cuff<-readCufflinks(gtfFile="merged.gtf",genome="grch38") cuff CuffSet instance with: 2 samples 56875 genes 282953 isoforms 131485 TSS 81720 CDS …
  • RNA-Seq analysis cummerbund package in R?
    written by Mask Mask
    RNA-Seq analysis cummerbund package in R? I performed RNA-Seq data analysis using protocol given in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3334321/. When I am using cummerbund package, it shows output …
  • Rna -Seq cummeRbund plot issues
    written by 1769mkc 1769mkc
    I'm using the tuxedo protocol for RNA-Seq data analysis the analysis is complete but it seems there are issues im not sure `CuffSet instance with: …
  • No CDS in Cuffdiff output !
    written by dina.hesham139 dina.hesham139
    Hey, I did and RNAseq analysis for 2 conditions, paired end experiments. Alignment was done with HISAT2 against hg38 and I followed cufflinks and cuffdiff …
  • From Cuffdiff Output to CummeRbund analysis/visualisation
    written by Wet&DryImmunology Wet&DryImmunology
    Hi,I had problem with using CummeRbund to analyse the output from Cuffdiff. I was trying to analysis RNA-seq using Cufflinks (I mean the suite). I …
  • Cummerbund Help
    written by madkitty madkitty
    <p>I have 3 samples in 3 folders under the working directory of R,</p> <ul> <li>~/Sample1 </li> <li>~/Sample2 </li> <li>~/Sample3</li> </ul> <p>How can I point to …
  • Cummerbund Returns 0 Sample
    written by madkitty madkitty
    <p>When running readcufflinks on the default folder containing our 3 samples it returns "0 sample". I tried readcufflinks on the sample folders provided by the …
  • Cummerbund Gene Tracking
    written by Eric • Eric
    Hello, I am having an issue with gene tracking in cummeRbund. Here is the cuff output: ```r > cuff CuffSet instance with: 4 samples 23285 …
  • Cuffdiff Output/Cummerbund
    written by Kaustubh • Kaustubh
    <p>Hi everyone,</p> <p>I want to analyze data using cummeRbund but I'm having problem with cuffdiff output. I don't get any entries in the gene<em>id and …