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  • Can I use htseq --samout file for subsequent annotation?

    Hi,
    So briefly what I'm doing is that:
    -->I'm annotating my smallRNA sequencing data using htseq-count.
    -->I'm using original.sam to annotate miRNAs and using -o to get the out.sam
    -->From that out.sam I can grep out the 'no_feature' reads/rows.

    The question:
    Maybe a stupid idea but is there any way I could use this out_no_feature.sam file for another round of htseq annotationagainst e.g. rRNA.gtf?

    As the out_no_feature.sam does not have a header, is there any way to reheader it or use the header from the original.sam file? Also, I guess I need to remove the last column "XF:Z:__no_feature" from the out_no_feature.sam

    Thanks ahead for comments and help

  • #2
    Hi Heso,

    You can use RSeQC's bam2fq.py to make a fastq file out of your "out_no_feature.sam".
    In order to get the header into your files, use:
    Code:
    samtools view -SH original.sam > header.txt
    Then use something like:
    Code:
    cat header.txt out_no_feature.sam | samtools view -bSh - > out_no_feature.bam
    . In case it was not sorted according to the position, you may need to include a samtools sort into the pipe.
    The "XF:Z"-field does not influence the downstream analysis. But since you have only alignments with this field will not give you any further information.

    Cheers,
    Michael
    Last edited by Michael.Ante; 05-18-2016, 03:42 AM. Reason: Typo

    Comment


    • #3
      Originally posted by Michael.Ante View Post
      Hi Heso,

      You can use RSeQC's bam2fq.py to make a fastq file out of your "out_no_feature.sam".
      In order to get the header into your files, use:
      Code:
      samtools view -SH original.sam > header.txt
      Then use something like:
      Code:
      cat header.txt out_no_feature.sam | samtools view -bSh - > out_no_feature.bam
      . In case it was not sorted according to the position, you may need to include a samtools sort into the pipe.
      The "XF:Z"-field does not influence the downstream analysis. But since you have only alignments with this field will not give you any further information.

      Cheers,
      Michael

      Thanks Michael, it worked perfectly!!

      /Helena

      Comment

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