I have finished pair-end RNAseq analysis using Tuxedo Protocol. Now I need to extract sequences of different isoforms of a gene from my samples (a total of 6).
How should I proceed?.
I guess I have to use *.bam, *.gtf files but how.?
I tried Genomicfeatures in R but it gets complicated for Arabidopsis and the commands are not so straightforward. If you have done something similar using genomicfeatures then I would appreciate if you can send me your script otherwise,
something java-based on web-based would be great. I dont have full command over command-prompt/python etc.