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  • Always run into problems with Cuffmerge

    Hi everyone,

    I always encounter problems when using Cuffmerge saying that it cannot find specific fasta records.

    I have downloaded both USCS mm9 and ENSEMBL from iGenomes, run top hat, cufflinks followed by cuffmerge.

    The command:
    Code:
    cuffmerge -g /data/projects/pospisilik/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.grep.gtf -s /data/projects/pospisilik/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa -p 8 assemblies.txt
    When I use mm9 I get:
    Warning: couldn't find fasta record for 'chr13_random'!
    Warning: couldn't find fasta record for 'chr17_random'!
    Warning: couldn't find fasta record for 'chr1_random'!
    Warning: couldn't find fasta record for.......

    When I use Ensembl, I get similar problems:


    Do you know what is going on here? I have tried to use grep command to remove all lines containing 'random' from the genes.gtf from mm9 iGenomes, but I am not sure if this is the way to do it.

    Thanks a lot!

    I really appreciate your help.
    Last edited by DonDolowy; 12-17-2012, 01:16 AM.

  • #2
    did you get any solution for this problem ?
    Originally posted by DonDolowy View Post
    Hi everyone,

    I always encounter problems when using Cuffmerge saying that it cannot find specific fasta records.

    I have downloaded both USCS mm9 and ENSEMBL from iGenomes, run top hat, cufflinks followed by cuffmerge.

    The command:
    Code:
    cuffmerge -g /data/projects/pospisilik/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.grep.gtf -s /data/projects/pospisilik/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa -p 8 assemblies.txt
    When I use mm9 I get:
    Warning: couldn't find fasta record for 'chr13_random'!
    Warning: couldn't find fasta record for 'chr17_random'!
    Warning: couldn't find fasta record for 'chr1_random'!
    Warning: couldn't find fasta record for.......

    When I use Ensembl, I get similar problems:


    Do you know what is going on here? I have tried to use grep command to remove all lines containing 'random' from the genes.gtf from mm9 iGenomes, but I am not sure if this is the way to do it.

    Thanks a lot!

    I really appreciate your help.

    Comment


    • #3
      I am just using the the grep´ed version of the genes.gtf where I have removed chr_random entries.

      Comment


      • #4
        Can you please tell me in a bit more detail (commands) because I am new in this field.
        Thank you

        Originally posted by DonDolowy View Post
        I am just using the the grep´ed version of the genes.gtf where I have removed chr_random entries.

        Comment


        • #5
          I am using UCSC mm9 genes.gtf from iGenome.

          I imagine I did something like:

          grep -v random genes.gtf > genes.grep.gtf

          Comment

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