Question: Difference between exon positions in hg19 and b37?
0
gravatar for mct2159
4.9 years ago by
mct21590
United States
mct21590 wrote:

I have a bunch of .bam files along with a .bed file containing the intervals for the exons. However, the .bam files are according to the b37 reference while the .bed file is according to the hg19 reference. If necessary, how can I convert the coordinates in the .bed file to a b37 reference?

sequencing alignment • 2.8k views
ADD COMMENTlink modified 4.9 years ago by Pierre Lindenbaum129k • written 4.9 years ago by mct21590
3
gravatar for Pierre Lindenbaum
4.9 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum129k wrote:

Use sed to convert the names. Devon wrote a github repo containing the names in each version: https://github.com/dpryan79/ChromosomeMappings/blob/master/GRCh37_UCSC2ensembl.txt

ADD COMMENTlink written 4.9 years ago by Pierre Lindenbaum129k
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