Question: Extract Negative chromosome(gene) location from VCF files
0
gravatar for MAPK
3.9 years ago by
MAPK1.5k
United States
MAPK1.5k wrote:

I have about 3000 genes list and their chromosome locations(start and end). Some of the locations have negative positions as you can see below in the table. I think this mean these genes are position referenced from negative strand. I need to extract these genes from VCF file, but there aren't any negative location in VCF file. Can someone please explain me how this issue could be addressed when extracting these gene locations from VCF files.

   gene_id symbol chromosome start_location end_location
1  "1"     "A1BG" "19"       " -58858171"   " -58864865"
2  "10"    "NAT2" "8"        "  18248754"   "  18258723"
3  "100"   "ADA"  "20"       " -43248162"   " -43280376"
4  "1000"  "CDH2" "18"       " -25530926"   " -25616549"
ADD COMMENTlink modified 3.9 years ago by Devon Ryan94k • written 3.9 years ago by MAPK1.5k
0
gravatar for Devon Ryan
3.9 years ago by
Devon Ryan94k
Freiburg, Germany
Devon Ryan94k wrote:

The negative positions are typically used to indicate the - strand. Yes this is incredibly unintuitive. So " -58858171" " -58864865" should be 58858171-58864865 on the - strand.

ADD COMMENTlink written 3.9 years ago by Devon Ryan94k
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