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Old 09-07-2011, 08:24 AM   #1
Junior Member
Location: Oslo

Join Date: Sep 2011
Posts: 1
Default no visual in Artemis and IGV


I am working with a small ribosomalRefernz"genome" to which i mapped an illumina data set from mirnas. i worked with novoalign and samtools and have all the files i need (ref, bam, bai) in the right folder, sorted as well and artemis will also open it, but just dont show anything where it is supposed to show it...i have no idea what that is

PLEASE HELP i am desperate.

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Old 09-08-2011, 09:22 AM   #2
Jim Robinson
Location: Boston, MA

Join Date: May 2009
Posts: 75


I can't speak for Artemis, but in IGV the usual cause for this is a mismatch in the chromosome (contig/sequence) names in the fasta file you used when defing the genome, and the corresponding names in the BAM file. You can patch this with an "alias" file as described in the user guide, let me know if you think this is the problem and need more details.
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