Changes between Version 3 and Version 4 of SOPs/homologous


Ignore:
Timestamp:
04/09/21 22:30:14 (4 years ago)
Author:
thiruvil
Comment:

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  • SOPs/homologous

    v3 v4  
    4040  * [[http://hgdownload.cse.ucsc.edu/goldenPath/hg19/multiz46way/alignments/|FASTA alignments of 45 vertebrate genomes with Human for CDS regions]]
    4141
     42==== liftOver ====
     43
     44[[https://genome.ucsc.edu/cgi-bin/hgLiftOver | UCSC LiftOver ]] can be used to convert, or lift over, genome coordinates within different assembly versions.  Alternatively, it can be used to convert between assemblies, though it may not convert correctly, e.g. due to rearrangements.
     45{{{
     46#command line
     47liftOver -minMatch=0.95 inputRegions.bed mm10ToHg38.over.chain.gz outRegionsConverted.bed failedConversions.bed
     48#set minMatch lower to relax the threshold for bases to remap
     49
     50}}}
     51
     52
    4253=== VISTA ===
    4354[[http://genome.lbl.gov/vista/index.shtml|VISTA]] also has genome-genome alignments available for download., but the last update appears to be May 2008.