getting the coordinates of mapped regions from a bam file
Once I mapped a genome to a reference genome, how can I get the mapped region coordinates and chromosome?
In addition, if possible, how can I get a bam file with the regions of the mapped + a padding (so maybe 2000kb above and below)?
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sciencercur •
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It looks like a homework; but anyways, I did not get the first part of the question, for the second part, did you try to look at bedtools?
What have you tried?
What does this mean? Please explain in more detail.
You get a BAM file from an alignment program. The BAM file will not give you any padding. Rather, you would read the BAM file - giving you an alignment position for each read. From this you can collapse (or reduce) overlapping reads to regions, and add padding using things like bedtools, R and the GenomicRanges library, etc. etc.