Hot to get alter splicing infomation from cufflink

[Luyi Tian]

for example: gene A have exon 1,2,3,4 in one condition and exon 1,2,4 in another condition. Could cufflink told us the structure of the two isoform(1234 and 124).

[colindaven]

I think so, if you have two separate BAM input files from tophat for cufflinks, then it should be able to generate the distinct isoforms - providing they are each restricted to one condition.