Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: [bam_parse_region] fail to determine the sequence name
0
gravatar for sekalazare
4.2 years ago by
sekalazare • 0
Netherlands
sekalazare • 0 wrote:

I'm trying to run differential expression using EdgeR and/or DEseq2 on the Ratsch Lab galaxy server but I keep getting this error:

 

[bam_parse_region] fail to determine the sequence name

 

I mapped the groomed and filtered FastQ files with Tophat2 using the mm10 reference and did DE expression with the Tophat2 bam files and the UCSC genes.gtf files.

 

Anyone know what could be the problem?
rna-seq identifiers gtf genomes bam • 1.5k views
ADD COMMENT • link •
modified 4.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.2 years ago by sekalazare • 0
1
gravatar for Bjoern Gruening
4.2 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:

Add which step it actually fail? During generation of the count matrix? This seems to be a samtools error that usually occurs if you mix chromosome or sequencing names from UCSC or EMBL.
ADD COMMENT • link written 4.2 years ago by Bjoern Gruening ♦ 5.1k

Agreed - this is most likely from SAMTools. More about sequence identifier mismatch issues is in the wiki link below. Just keep in mind that the other public server may have content in the reference genome mm10 that differs from the public Main Galaxy instance at http://usegalaxy.org. Contact that group for details you can't obtain from converting the mapped results in BAM-to-SAM format. Identifiers must be the same between all inputs - GTF, Reference genomes, BAM inputs, anything else.
https://wiki.galaxyproject.org/Support#Reference_genomes

Best, Jen, Galaxy team

ADD REPLY • link written 4.2 years ago by Jennifer Hillman Jackson ♦ 25k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 166 users visited in the last hour