Question: Sequences of isoforms of a gene from RNAseq data
gravatar for mfahim
4.7 years ago by
Korea, Republic Of
mfahim10 wrote:

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.



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