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  • Cuffdiff Error Unrecognized file type (bam file)

    Hey All, Using the following command for cuffdiff I get the error
    Error: cannot open file /home/yelab/leanne/Projects/Xu_RNASeq/F4_Alignment/LS/LS_XXM_AGG_THout/accepted_hits.bam for reading. Unrecognized file type


    COMMAND
    cuffdiff -o diff_out ./F6_Cuffmerge/LS/merged_asm/merged.gtf \ /home/yelab/leanne/Projects/Xu_RNASeq/F4_Alignment/LS/LS_XXM_AGG_THout/accepted_hits.bam \ /home/yelab/leanne/Projects/Xu_RNASeq/F4_Alignment/LS/LS_XXM_AGG_THout/F4_Alignment/LS/LS_XYM_AGG_THout/accepted_hits.bam


    Any help would be greatly appreciated !

    Leanne

  • #2
    As you posted the command, without any new lines, and two white spaces (one before and one after the backslash), the syntax is incorrect.

    You need to add the new lines and remove the extra white space

    Code:
    cuffdiff -o diff_out ./F6_Cuffmerge/LS/merged_asm/merged.gtf \ 
    /home/yelab/leanne/Projects/Xu_RNASeq/F4_Alignment/LS/LS_XXM_AGG_THout/accepted_hits.bam \ 
    /home/yelab/leanne/Projects/Xu_RNASeq/F4_Alignment/LS/LS_XXM_AGG_THout/F4_Alignment/LS/LS_XYM_AGG_THout/accepted_hits.bam
    If you're still experiencing problems, check that the file exists.
    Code:
    ls /home/yelab/leanne/Projects/Xu_RNASeq/F4_Alignment/LS/LS_XXM_AGG_THout/accepted_hits.bam
    Also, check that the file is indeed a BAM file.
    Code:
    samtools view -h /home/yelab/leanne/Projects/Xu_RNASeq/F4_Alignment/LS/LS_XXM_AGG_THout/accepted_hits.bam | more
    Last edited by blancha; 06-13-2014, 10:13 AM.

    Comment


    • #3
      Thanks Alot!

      Comment

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