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  • sarbashis
    Member
    • Jun 2010
    • 17

    Help in samtools

    Hi all,
    I am using samtools to visualize my alignment. I used the following command
    ./samtools tview <*bam> <*ref.fasta>

    could any one tell me, how to use g (goto) to visualise a specific location. I have tried chr1:1000-2000, but nothing happened. Thanks in advance
  • ulz_peter
    Senior Member
    • Feb 2010
    • 219

    #2
    Probably your reference sequence is not called "chr1" but "1". Another issue could be that your alignment files do not use the same name for the reference sequences.
    UCSC calls it's hg19 files chr1, chr2,
    ensembl describes them as 1,2,3

    That's just for human alignments, I don't know which organism you are working on.

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