Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Cuffmerge Error ercfrtz Bioinformatics 12 05-19-2014 09:02 PM
cuffmerge problems ccstaats Bioinformatics 0 02-02-2012 04:28 AM
cuffmerge problem camelbbs RNA Sequencing 0 11-06-2011 04:58 PM
Questions about cuffmerge Jolin Bioinformatics 0 10-04-2011 12:46 AM
Cuffdiff outputs mostly FAIL agc Bioinformatics 0 01-11-2011 04:45 AM

Thread Tools
Old 07-31-2011, 03:01 PM   #1
Senior Member
Location: berd

Join Date: Dec 2010
Posts: 181
Default cuffmerge fail

Hi ,
i am trying to use cuffmerge from Cufflinks after doing all steps in "getting started page"
in the 3 step when i was trying to merge , i am having this error:

[Sun Jul 31 22:53:56 2011] Beginning transcriptome assembly merge

[Sun Jul 31 22:53:56 2011] Preparing output location ./merged_asm/
Warning: no reference GTF provided!
[Sun Jul 31 22:53:56 2011] Converting GTF files to SAM
[22:53:56] Loading reference annotation.
[22:53:56] Loading reference annotation.
[Sun Jul 31 22:53:56 2011] Assembling transcripts
You are using Cufflinks v1.0.3, which is the most recent release.
[bam_header_read] EOF marker is absent.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
File ./merged_asm/tmp/mergeSam_fileuL7Jzz doesn't appear to be a valid BAM file, trying SAM...
Error: sort order of reads in BAMs must be the same
Error: could not execute cufflinks

how can i solve it?
do i have to sort some files?

thank in advance..
papori is offline   Reply With Quote

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 05:00 PM.

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