Useful tips and information

Little tidbits of information with no other clear place to post them

• Cheat sheet for different co-ordinate systems used by browsers https://www.biostars.org/p/84686/

QC tests to implement when programming/automating genomic tasks

• check gene/snp names are correct

  • check for extra whitespace
  • check for genes/snps that don't match anything

• check consistent formatting of regions

  • do regions use a 0 or 1 based index system
  • consistency of format

• check positions

  • are they the same genome build
  • are they on the usual chromosomes
  • do you get/want alternate mappings

• check for strand issues

  • is strand important

• check for duplication of genes/regions/snps

  • check input and outputs

• visualise your results (if possible)

  • UCSC custom tracks are very useful

• regular expressions

  • make sure they match what you think they match
  • be defensive against matching things you don't want

Gene Synonyms

This file can be used to find synonyms for genes ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz

Working on the server

copy from one volume to another using the xsan cp command

/usr/cvfs/bin/cvcp -d -t 16 -xzy <source> <target>