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  • Error occured in matchAnnot.py

    Hi there,
    A ERROR occurred during running matchAnnot.py by using human genome hg38 and annotation file v.25. The error message said "chromosome 10 not in annotation" but it actually exist in gtf file. However, there is no such a problem when apply genome hg19 and GTF file v.19. I googled it, someone came across the same one but no perfect answer to solve it. Any help would be appreciated!
    Click image for larger version

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  • #2
    Originally posted by lingling huang View Post
    Hi there,
    A ERROR occurred during running matchAnnot.py by using human genome hg38 and annotation file v.25. The error message said "chromosome 10 not in annotation" but it actually exist in gtf file. However, there is no such a problem when apply genome hg19 and GTF file v.19. I googled it, someone came across the same one but no perfect answer to solve it. Any help would be appreciated!
    [ATTACH]4493[/ATTACH]

    This is really a question for the author of the software, MatchAnnot, Tom Skelly.

    Python scripts for matching output of Pacific Biosciences IsoSeq RNA-seq pipeline to an annotation file. - TomSkelly/MatchAnnot


    Without seeing your annotations dataset, all I can say is make sure the chromosome names match identically. e.g. (upper case vs lower case characters)

    Comment


    • #3
      Originally posted by gconcepcion View Post
      This is really a question for the author of the software, MatchAnnot, Tom Skelly.

      Python scripts for matching output of Pacific Biosciences IsoSeq RNA-seq pipeline to an annotation file. - TomSkelly/MatchAnnot


      Without seeing your annotations dataset, all I can say is make sure the chromosome names match identically. e.g. (upper case vs lower case characters)
      I have attached screenshot message. Why the result are totally different by using samtools sort and just sort.
      Click image for larger version

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      Click image for larger version

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      Click image for larger version

Name:	matchAnnote25.png
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ID:	305156
      I look the name of chromosome by using basic Unix commands such as:

      > cut -f1 gencode.v25.chr_patch_hapl_scaff.annotation.gtf | grep -v '^#' | sort | uniq | less
      chr1
      chr10
      chr11
      chr12
      chr13
      chr14
      chr15
      chr16
      :
      :

      etc.

      See, chr10 is actually exist. if the name must be chromosome not chr ,I think the error should first be "chromosome 1 not in annotation ".

      Comment


      • #4
        Originally posted by lingling huang View Post
        I have attached screenshot message. Why the result are totally different by using samtools sort and just sort.
        [ATTACH]4494[/ATTACH]

        [ATTACH]4495[/ATTACH]

        [ATTACH]4496[/ATTACH]
        I look the name of chromosome by using basic Unix commands such as:

        > cut -f1 gencode.v25.chr_patch_hapl_scaff.annotation.gtf | grep -v '^#' | sort | uniq | less
        chr1
        chr10
        chr11
        chr12
        chr13
        chr14
        chr15
        chr16
        :
        :

        etc.

        See, chr10 is actually exist. if the name must be chromosome not chr ,I think the error should first be "chromosome 1 not in annotation ".
        Again, MatchAnnot was written by a third party developer, your question would be better addressed to the author of the software as an issue in the github page I linked in my first post.

        This question has already been asked there in the past:
        While requiring all the chromosome names in the gtf file makes sense, can this error be considered replaced with a warning along with skipping entries from the missing chromosomes? Otherwise it req...

        Comment


        • #5
          Originally posted by gconcepcion View Post
          Again, MatchAnnot was written by a third party developer, your question would be better addressed to the author of the software as an issue in the github page I linked in my first post.

          This question has already been asked there in the past:
          https://github.com/TomSkelly/MatchAnnot/issues/6
          Thank you for reply! But there was no reply!

          Comment

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