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Old 05-24-2013, 01:51 AM   #1
Triple_W
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Default Tophat result: how to get the number for novel junctions

hi,

tophat can output a file junctions.bed including the splicing sites for junction reads.
Can I get novel splicing sites that tophat identified from known ones given by reference gene annotations?
Any suggestions would be appreciated.
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Old 07-03-2013, 12:44 AM   #2
Triple_W
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Default can cuffdiff handle the samples with different treatments and a time series?

any suggestions?

Last edited by Triple_W; 07-03-2013 at 12:51 AM.
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