rna-seq tiling reads

[adrian]

Hi:

I found interesting exon skip events from my rna-seq experiments. My next aim to reconstruct possible an ORF with and without exon skip.

I tried velvet and Transdecoder. However the issue is these algorithms are constructing longest possible orf, 5' and 3'. This is not what I am looking for.

For condition 1 -
Given start and end of gene coordinates, considering an exon is skipped between these two points, I want to walk over reads with and without exon that is skipped in condition 2.

Subsequently I want to translate to see if they are in coding context.

Is there any software for such walking on rna-seq reads and reconstructing an orf.

thanks
Adrian

[dpryan]

Do you have a GTF or GFF file? If so, you could use GenomicRanges. The workflow would be something like:
1) Load annotation
2) Extract only the gene of interest, this just makes getting the sequences faster
3) getSeq() to get the sequences
4) Write the sequences of the CDS that you want for each condition to separate files

That should be relatively straight forward if you're familiar with R.

[adrian]

Hi Devon,
Thanks for the tip. I am familiar with R.
I will try genomicRanges.

Thanks
Adrian