HI I was using UCSC liftover tool to lift the mm8 version to mm10. The following is the trial data that i gave. the difference between the start and end positions (2nd and 3rd columns) is around 1000bps.
chr17 14696791 14697791
chr17 33422990 33423990
chr17 27382883 27383883
chr17 25971254 25972254
chr17 44970114 44971114
However when i have converted to mm10 i observed something like this
**chr17 14960215 14992839**
chr17 33817030 33818030
chr17 27655294 27656294
chr17 26243654 26244654
chr17 45506533 45507533
The first row (highlighted with **) the difference between start and end was around 32 kb. Not sure what was happening. The options that i used were
Minimum ratio of bases that must remap: 0.95
Minimum hit size in query: 0
Minimum chain size in target: 0
Min ratio of alignment blocks or exons that must map: 1
and i kept Allow multiple output regions option unchecked
•
written
by
ancient_learner
I tried the conversion of the first coordinates doing mm8 --> mm9 --> mm10
And for the first coordinates it gives:
Each times with a 1000bps difference.
Moreover, the DNA sequences (1) and (3) are the same (with ~6 mismatches)
Thank you very much. Does this mean that i should not convert directly from mm8 to mm10? Because i have done many of my previous works this way will they be wrong?
I think you should do it sequentially. Here is one answer I found from UCSC Genome Bioinformatics Group member.
That is exactly right: you should do sequential lifts from mm6 -> mm8 -> mm9 -> mm10.
Log in to answer this question.