alternative splicing detection from one sample

[atma_weapon]

hello, I would like to know if it is possible to check if in a rna-seq there are alternative splicing events, not comparing two condition but inside one condition only, that is if different transcript isoforms are produced in the same sample, thank you

[mojo1028]

isoform detection

Check out Enzymatics AMP technology with individual cDNA molecule tagging. It will resolve your isoforms

[blancha]

Cufflinks will compute the expression levels of individual isoforms.
Or, you can just examine the alignment files for individual genes in IGV (or the UCSC Genome Browser).
Obviously, it is not always possible to determine accurately to which transcript a read belongs, so the results are sometimes ambiguous.

[mojo1028]

cDNA tagging for isoform detection

Cufflinks will compute the expression levels of individual isoforms.
Or, you can just examine the alignment files for individual genes in IGV (or the UCSC Genome Browser).
Obviously, it is not always possible to determine accurately to which transcript a read belongs, so the results are sometimes ambiguous.

Enzymatics AMP technology labels each cDNA with an adapter containing a unique random 8-mer sequence prior to amplification and NGS. This allows you to examine specific isoforms within the sequencing data. Check it out at www.enzymatics.com