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Where can I get a gene list of Arabidopsis in RefSeq format?

Hello! I am a plant guy. I would like to use DepthOfCoverage tool to analysis my sequencing data. But there is no gene list of Arabidopsis in UCSC genome table browser. Where can I get a gene list of Arabidopsis in RefSeq format?

Best Answers

Answers

  • SkyWarriorSkyWarrior ✭✭✭ TurkeyMember ✭✭✭

    Is GFF format ok for you?
    I am attaching TAIR10 to this post. From IGV directly.

  • Thanks! @ SkyWarrior
    But I need txt format for DepthOfCoverage. Or how can I transfer GFF to the format that is suitable for DepthOfCoverage?

    The provided gene list must be of the following format:

    585 NM_001005484 chr1 + 58953 59871 58953 59871 1 58953, 59871, 0 OR4F5 cmpl cmpl 0,
    587 NM_001005224 chr1 + 357521 358460 357521 358460 1 357521, 358460, 0 OR4F3 cmpl cmpl 0,
    587 NM_001005277 chr1 + 357521 358460 357521 358460 1 357521, 358460, 0 OR4F16 cmpl cmpl 0,
    587 NM_001005221 chr1 + 357521 358460 357521 358460 1 357521, 358460, 0 OR4F29 cmpl cmpl 0,
    589 NM_001005224 chr1 - 610958 611897 610958 611897 1 610958, 611897, 0 OR4F3 cmpl cmpl 0,
    589 NM_001005277 chr1 - 610958 611897 610958 611897 1 610958, 611897, 0 OR4F16 cmpl cmpl 0,
    589 NM_001005221 chr1 - 610958 611897 610958 611897 1 610958, 611897, 0 OR4F29 cmpl cmpl 0,

  • Thank you very much! @ SkyWarrior
    Could you tell me which tool or setting are used for this conversion?

  • SheilaSheila admin Broad InstituteMember, Broadie, Moderator admin

    @zhiyewang1
    Hi,

    I think if you google gff to bed, you will get some helpful hints.

    -Sheila

  • Hello!
    I have another issue.

    When I run DepthOfCoverage, a user error occurred: "DepthOfCoverage " is not a valid command.
    My command line is:
    ./gatk DepthOfCoverage -R TAIR10_genomic.fa -o Sample-1/ -I Sample1_uniq_reads.bam -geneList TAIR10_GFF3_genes_transposons_sort.bed

    The version of GATK is 4.0.3.0
    How can I fix it?

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