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  • Locale settings

    Hi all,

    What locale(s) are recommended for lab servers? We primarily work in applied genomics (think off-the-shelf programs, scripting, R).

    I just ran into the whole locale issue when sorting a pair of FASTQ files by read ID. Apparently my default "en_US.UTF-8" locale ignores colons and other punctuation. So I switch to "C", and if so, will this have any unintended consequences?

    Thanks!

  • #2
    I believe GATK and samtools sort read names differently anyway - but that's a good point about the locale having an input.

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    • #3
      Yeah, most programs (should) do a byte-by-byte comparison but unix sort is affected by locale:
      *** WARNING *** The locale specified by the environment affects sort order. Set LC_ALL=C to get the traditional sort order that uses native byte values.

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      • #4
        I would stick to LC_ALL=C for the reasons mentioned by fanli. Half the time that people report problems with deepTools to us it's because of this.

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