Hello, I have sequences of similar chromosomes for different species that I want to compare. I would like to be able to generate a conservation track such as the one seen here: http://tinyurl.com/yz6o6fu
I looked at an example of steps to be taken. Could you please verify/clarify for me? Let's assume I want to compare 2 chromosomes. 1. Mask both chromosomes 2. Align both chromosomes with blastz 3. Chain using axtChain (QUESTION: I see this program takes two directories as arguments. If I wish only to compare two chromosomes, would these directories have only one file each?) 4. Get size of each chromosome for chain filtering using faSize 5. Sort and filter chains a. use chainMergeSort using chain from step 3 b. prenet with chainPreNet using chain from 5.a., size of target chromosome gotten from step 4, and size of query chromosome from step 4 as arguments 6. Netting? 7. Convert to .maf and use phyloFit 8. Run phastCons to get .wig output which can be uploaded as a conservation track Since I am only comparing two chromosomes at a time, I think only a single chain is generated which doesn't have to be netted. Am I missing anything? Thanks, Bremen _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
