2.9 years ago by
Maybe ignore the original post - the reads are single end? What mapping tool was used? The tag "XS" must be present in the input BAM datasets for Cuffdiff. If the reads are not from a known, stranded, sequencing procedure, assigning this value will only be possible if the sequence overlaps an intron during mapping (contains a splice site). Tophat will assign this value during the mapping run. If you used another mapper, check the documentation or simply convert the BAM to SAM and examine. This missing value could produce the error you describe above.
===> original post
Where are you working? http://usegalaxy.org, a cloud, a local, or another public server?
The data either did not load properly or was malformed prior to upload. Try uploading again. If problematic, test the data locally with something simple like Samtools to make certain that it is intact. Also - please remember - when loading BAM datasets into Galaxy, just load the .bam. The .bam.bai index is created on the Galaxy server as part of the metadata detection processing.
Also, once you have this going, consider using a iGenomes reference annotation file with this tool suite. These files contain specific attributes utilized to generate the full compliment of statistics. Data for mm9 is available.
iGenomes reference annotation
mm9 happens to also be already included on Galaxy Main usegalaxy.org). Shared Data -> Data Libraries -> iGenomes
Best, Jen, Galaxy team