What is the command line to map XLOC_ids from cufflinks with rice LOC_ids from msu

Question

[isha.lily20]

Hello Researchers

What is the command line to map XLOC_ids from cufflinks with rice LOC_ids from msu rgap 7

means i want a resultant excel sheet with XLOC_ids having similar loc_ids

input i have list of XLOC_ids and LOC_ids seperately

Thank you for the intellectual help

Answer 1

[IrisChang]

The XLOC to LOC_id map will be generated in the .diff file of cufflink output. So you could just use cut to grab the information you want.

[isha.lily20]

Hello Iris

I cant take from cuffdiff, i have to use only cuffmerge data because not working on differential expression

I have genome.fa of rice reference genome

and have to map with tcons of cuffmerge data is question

Thank you so much for any intellectual/ technical help