How To Combine Fpkm Values From Cufflinks With Contigs From De Novo Assembly Program Velvet/Oases?

Question

[User 6181]

Hi all,

I am working on RNA-seq data analysis. I've finished running Tophat and Cufflinks to get FPKM values for each read from Illumina pair-end sequence. Also, parallely I've run Velvet to get contig sequences through de novo assembly and Gmap to see if the assembled sequences map to reference genome (this reference genome is not complete for now, but somewhat useful). Now, I am trying to combine all information so I can have sequence information for a contig and FPKM value for the corresponding to the contig. Some suggested I can convert Cufflink and Gmap outputs to bedfiles and then use IntersectBed to see if there's any overlap. However, I am not sure how I can have every information saved in the output from Bedtools. IntersectBed default seems to provide me overlapped region with 'A' file as a template, so I couldn't see any information from 'B' file. Is there any solution for me?? Please let me know. I would appreciate for your suggestion!

Answer 1

[Rlong]

You are probably looking for the option "-wo" on intersectBed:

 -wo     Write the original A and B entries plus the number of base
         pairs of overlap between the two features.
         - Overlaps restricted by -f and -r.
         Only A features with overlap are reported.