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Old 03-15-2011, 02:15 PM   #1
doublealice
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Default Import BAM into JBrowse

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!

Last edited by doublealice; 03-15-2011 at 02:18 PM.
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Old 03-16-2011, 07:30 AM   #2
doublealice
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I'd tried to look for the answer whole day but failed. I appreciate the help from you in advance. Please hint. Thanks!
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Old 03-16-2011, 09:34 AM   #3
kmcarr
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Default

Quote:
Originally Posted by doublealice View Post
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?
Yes, it does.

Quote:
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!
Simply try running the program with no options or files listed on the command line. You will see the usage details.
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Old 03-16-2011, 09:58 AM   #4
doublealice
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Thanks! I ran it and found it needed two pm modules. I installed it from CPAN and it works! Thank you !
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