SAMTools alignment viewer

Fred13

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Join Date: Nov 2009

Posts: 9
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SAMTools alignment viewer

11-30-2009, 06:09 AM

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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