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  • Fred13
    Junior Member
    • Nov 2009
    • 9
    #1

    SAMTools alignment viewer

    Hi everybody ...

    We have sequence fragments of a mutant nematode that we sent to sequenced. We used MAQGene to link fragments genome to the reference sequence of C. elegans. Then we used maq2sam-long to convert the .map file into a .sam file. With SAMTools I can visualize the alignment with tview. There is on the top the reference sequence and down all the fragments with overlap if present. I would like to know what kind of alignment browser allows sam (or bam) file. I try to use Integrative Genomics Viewer (IGV) but I can't see the aligment as in tview : the reference sequence up and all the other sequences down. Or if there is a possibility to generate a text file with the alignment of tview ?

    Thanks to the person reading this and sorry if the question is stupid ....
    Tags: alignment, elegans, genome, maqgene, samtools
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