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  • lwhitmore
    Member
    • Aug 2013
    • 70
    #1

    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
    Tags: None
    • blancha
      Senior Member
      • May 2013
      • 367
      #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

        • lwhitmore
          Member
          • Aug 2013
          • 70
          #3
          Thanks Alot!

            Comment

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