How to convert a list with SNP gene positions into the list with gene names?
How to convert a list with SNP gene positions into a list with gene names?
List of SNPs (Betula carelica):
- PLASTID 25516 25516 1 C PLASTID 25557 25557 1 /
PLASTID 25570 25570 1 / PLASTID 25572 25572 1 /
PLASTID 25578 25578 1 / PLASTID 25592 25592 1 A
PLASTID 25595 25595 1 A PLASTID 25599 25599 1 T
PLASTID 25607 25607 1 / PLASTID 25626 25626 1 A
PLASTID 25631 25631 1 / PLASTID 25632 25632 1 C
PLASTID 25642 25642 1 C PLASTID 25666 25666 1 T
PLASTID 25677 25677 1 T PLASTID 25679 25679 1 A
PLASTID 25682 25682 1 A PLASTID 25685 25685 1 G
PLASTID 25687 25687 1 C PLASTID 25691 25691 1 A
PLASTID 25692 25692 1 C PLASTID 25700 25700 1 A
PLASTID 25702 25702 1 GA PLASTID 25726 25726 1 C
PLASTID 25728 25728 1 G PLASTID 25738 25739 1 /
PLASTID 25747 25747 1 C PLASTID 25750 25750 1 /
PLASTID 25752 25753 1 / PLASTID 25771 25771 1 /
PLASTID 25781 25781 1 T PLASTID 25782 25782 1 TC
PLASTID 25787 25787 1 C
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matveyspr •
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matveyspr •
1 answer
bedtools intersect is available in Galaxy ("BEDTools | Intersect Intervals") and can do this. You need 2 files:
- a file containing SNP positions (like you have it but only 1 SNP per line) in BED format
- a second file containing gene annotation (start and end positions of exons or genes) in GFF or BED format. Usually you can get this from the sequencing project websites or consortium). If not available create it yourself in the format Chromosome StartPos Endpos GeneName using a text editor
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