Dear all,
I am learning JBrowse for visualizing my genome mapping, follow 'JBrowse getting started guide' at http://jbrowse.org/code/jbrowse-master/docs/tutorial/
I was stuck when I tried to import a BAM file into JBrowse.
Here is the command:
bin/flatfile-to-json.pl --bam my.sort.bam --tracklabel bam_simulated --key "Simulated next-gen reads" --cssClass basic --clientConfig '{"featureCss": "background-color: #66F; height: 8px", "histCss": "background-color: #88F"}'
The output is:
BAM support has been moved to a separate program: bam-to-json.pl at ./bin/flatfile-to-json.pl line 133.
Does it mean I should use bam-to-json.pl to import BAM file? But I cannot find out the usage or parameter setting on bam-to-json.pl. Can anybody help me work it out? Thank you very much!
I am learning JBrowse for visualizing my genome mapping, follow 'JBrowse getting started guide' at http://jbrowse.org/code/jbrowse-master/docs/tutorial/
I was stuck when I tried to import a BAM file into JBrowse.
Here is the command:
bin/flatfile-to-json.pl --bam my.sort.bam --tracklabel bam_simulated --key "Simulated next-gen reads" --cssClass basic --clientConfig '{"featureCss": "background-color: #66F; height: 8px", "histCss": "background-color: #88F"}'
The output is:
BAM support has been moved to a separate program: bam-to-json.pl at ./bin/flatfile-to-json.pl line 133.
Does it mean I should use bam-to-json.pl to import BAM file? But I cannot find out the usage or parameter setting on bam-to-json.pl. Can anybody help me work it out? Thank you very much!
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