Question: [bam_parse_region] fail to determine the sequence name
0
gravatar for sekalazare
3.4 years ago by
sekalazare0
Netherlands
sekalazare0 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 • 1.2k views
ADD COMMENTlink modified 3.4 years ago by Jennifer Hillman Jackson23k • written 3.4 years ago by sekalazare0
1
gravatar for Bjoern Gruening
3.4 years ago by
Bjoern Gruening4.8k
Germany
Bjoern Gruening4.8k 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 COMMENTlink written 3.4 years ago by Bjoern Gruening4.8k

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 REPLYlink written 3.4 years ago by Jennifer Hillman Jackson23k
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