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  • GATK convert SAM to BAM

    Following the GATK example but the spacing seems off in the command. Is it and how do I correct it? Thanks

    Code:
    java -jar picard.jar SortSam \ 
         INPUT=/home/cmccabe/IDP/mapped_unmatched_adapter_removed_quality_trimmed_NA12878-NextSeq-S1_R1_and_R2.sam \ 
         OUTPUT=/home/cmccabe/Desktop/NGS/picard-tools-1.139/sorted_mapped_unmatched_adapter_removed_quality_trimmed_NA12878-NextSeq-S1_R1_and_R2.bam  \ 
         SORT_ORDER=coordinate

  • #2
    the spacing looks OK to me.

    Comment


    • #3
      Here is what it looks like in the ubuntu terminal:

      Code:
      cmccabe@DTV-A5211QLM:~$ java -jar picard.jar SortSam \ 
      Error: Unable to access jarfile picard.jar
      cmccabe@DTV-A5211QLM:~$      INPUT=/home/cmccabe/IDP/mapped_unmatched_adapter_removed_quality_trimmed_NA12878-NextSeq-S1_R1_and_R2.sam \ 
       : command not found
      cmccabe@DTV-A5211QLM:~$      OUTPUT=/home/cmccabe/Desktop/NGS/picard-tools-1.139/sorted_mapped_unmatched_adapter_removed_quality_trimmed_NA12878-NextSeq-S1_R1_and_R2.bam  \ 
       : command not found
      cmccabe@DTV-A5211QLM:~$      SORT_ORDER=coordinate
      cmccabe@DTV-A5211QLM:~$ echo $PATH
      /home/cmccabe/Desktop/NGS/bedops-2.14.4/bin:/home/cmccabe/Desktop/NGS/samtools-1.2:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/home/cmccabe/Desktop/NGS/bedtools2-25.0/bin:/home/cmccabe/Desktop/NGS/bbmap-35.59:/home/cmccabe/Desktop/NGS/FastQC-0.11.4:/home/cmccabe/Desktop/NGS/picard-tools-1.139
      Thank you .

      Comment


      • #4
        Just delete the extra white spaces.
        You can use a text editor that displays white space to make your life easier.
        I like TextWranger on Mac, which has the option to display white spaces.

        Code:
        java -jar picard.jar SortSam \
        INPUT=/home/cmccabe/IDP/mapped_unmatched_adapter_removed_quality_trimmed_NA12878-NextSeq-S1_R1_and_R2.sam \
        OUTPUT=/home/cmccabe/Desktop/NGS/picard-tools-1.139/sorted_mapped_unmatched_adapter_removed_quality_trimmed_NA12878-NextSeq-S1_R1_and_R2.bam \
        SORT_ORDER=coordinate

        Comment


        • #5
          I use notepad++ with ubuntu and it is hard to see the spaces in yellow (not sure why this color was used). Thank you .

          Comment

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