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  • samtools on centos

    Dear all,

    I have compiled and installed samtools as per the standard instructions given. When i tried to fetch sub region of a sequence it is giving the header only.

    I am using the command

    samtools faidx test.fasta

    to create index file and then to fetch the sequence

    samtools faidx test.fasta Wheat:5-15

    This is just printing the fasta header and not fetching the sequence
    >Wheat:5-15


    Please help.....

  • #2
    Please reply guys.. Where I am committing mistake??? Please help..

    Comment


    • #3
      What happens if you type:

      Code:
      grep -A 1 Wheat test.fasta

      Comment


      • #4
        Thanks

        Thanks for the response.

        Somehow samtools has started working fine automatically. I have not made any changes.

        Thanks to establish such a nice forum...

        Comment


        • #5
          In reply to Pryan,

          It is giving the first line of the fasta file of Wheat header. Anyhow samtools has started working all fine on its own.

          Thanks for your support.

          Comment

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