Question: Cuffdiff Error - sort order of reads in BAMs must be the same
2
gravatar for francis.gandhi
2.9 years ago by
United States
francis.gandhi20 wrote:

Hi,

I am trying to run Cuffdiff with a Cuffmerged data of 8 files along with their Tophat counterparts and am coming up with an Error "sort order of reads in BAMs must be the same". Will be awesome if I can get some guidance to get this issue fixed.

Cheers

Francis

rna-seq cuffdiff • 2.7k views
ADD COMMENTlink modified 10 months ago by takshan10 • written 2.9 years ago by francis.gandhi20
0
gravatar for Jennifer Hillman Jackson
2.9 years ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

It could be the ordering of the data in the input reference dataset (GTF or GFF3). This workflow can be used to sort it correctly for this tool. All steps that use it will need to be executed again (Cufflinks, if used there - and Cuffmerge).
http://usegalaxy.org/u/jeremy/p/transcriptome-analysis-faq#faq5

The source does not need to be Ensembl, but the reference genome the GTF/GFF3 data is based on must be an exact match for the reference genome specified with any tool (if/when used). Meaning, the chromosome identifiers must be exactly the same. In Cuffdiff, this is used when "Bias correction" is checked. Avoid that option if the reference genome is not a match for one in Galaxy and you are not providing it as a Custom Reference Genome. How to check versus Galaxy native genomes or add a Custom reference:
http://wiki.galaxyproject.org/Support#Reference_genomes
http://wiki.galaxyproject.org/Support#Custom_reference_genome

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.9 years ago by Jennifer Hillman Jackson23k

Thank you so much for the information Jennifer. I will give it a shot.

Cheers, Francis

ADD REPLYlink written 2.9 years ago by francis.gandhi20

Thanks Francis! If this works, it would be great if you could "accept" the answer so that others may easily find it. Just click on the checkmark next to the answer. Much appreciated! Jen

ADD REPLYlink written 2.9 years ago by Jennifer Hillman Jackson23k
0
gravatar for takshan
10 months ago by
takshan10
India
takshan10 wrote:

Am also having the same issue. am unable to RUN the workflow provided in FAQ to sort also using sort sam/bam am unable to use in cuffdiff. Any guidance would be of great help.

ADD COMMENTlink written 10 months ago by takshan10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 76 users visited in the last hour