From the transcriptomic data of a plant generated under different physiological conditions,I need to analyze the alternative splicing including its quantification.
What insilico strategy would be the best and easy?
Thanks.
If you are working with model organisms for which there are reference genomes, you can try cufflinks (http://cole-trapnell-lab.github.io/cufflinks/tools/), or stringtie (https://ccb.jhu.edu/software/stringtie/), also referenced commonly as the tuxedo tools. Note that you will probably need a few of the other tuxedo tools, such as bowtie, etc. But those websites provide good guides for beginners.
Additionally, you can try this that showed up in my feed not too long ago. Seems worth exploring. http://sjcockell.me/2015/05/18/alignment-free-transcriptome-quantification/
DEXSeq - count based data - comparing the counts in exons to the counts in the gene
cufflinks - taking the exon junction knowlegde into account - to find what isoforms or novel transcripts you have
MISO with sashimi plots (yummy!) - for combining the coverage and junction information
Sailfish - isoform quantification if you trust your annotation (not likely to be good for plants, other than AT perhaps)
and loads of viewing in IGV :) Good luck!
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