Question: creating BAM? alignment files for IGV
gravatar for ad
4.4 years ago by
United States
ad30 wrote:

Hi, I have coordinate data for several sequences I want to align against genomes in IGV. The preferred format for alignment is said to be BAM. Unfortunately I haven't found a straightforward way of creating BAMs straight from coordinates. I assume I'll need the reference genome as well. Is there any simple way to do it from R/Bioconductor?

myposts alignment R genome • 1.2k views
ADD COMMENTlink written 4.4 years ago by ad30

Do you have sequences you want to align, or do you have sequences (whose coordinates you know already) which you to display? If you have the genomic coordinates, all you need is a tab-delimited .BED file with:

chromName     gene1StartPos      gene1EndPos
chromName     gene2StartPos      gene2EndPos

And yes, to display on IGV you do need the reference genome.

ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by h.mon29k
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