Question: How do I associate a genome with a BAM file?
1
gravatar for mike.thon
2.8 years ago by
mike.thon30
University of Salamanca, Spain
mike.thon30 wrote:

I aligned some RNA-Seq reads to a genome sequence using tophat2 and now cuffdiff complains that there are no genome sequences associated with the BAM files.  The genome sequence is a fasta file that I imported into my history.  If I edit the BAM file's attributes to set the genome sequence, I am only presented with a list of 'built in' genome builds. How do I set the genome sequence for these BAM files?

 

tophat tophat2 bam • 993 views
ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by mike.thon30
2
gravatar for mike.thon
2.8 years ago by
mike.thon30
University of Salamanca, Spain
mike.thon30 wrote:

I will answer my own question.

The custom genome can be added under User -> Custom Builds.

More instructions are here: https://wiki.galaxyproject.org/Learn/CustomGenomes#Custom_Builds

 

ADD COMMENTlink written 2.8 years ago by mike.thon30
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