Indexing

Question

[GG]

Hello,

I have the following table schema.

For negative strands, how would the indexing work? Would chromEnd be 0 based and chromStart be non-inclusive? This is from the UCSC genome table browser. Thank you in advance for your answer!

[Pierre Lindenbaum]

how would the indexing work?

what 'indexing' are you talking about ?

[GG]

I mean 0 based and 1 based indexing as well as it being non-inclusive and inclusive. So I am wondering whether chromEnd (so transcription start for -ve strand genes) would be 0 based and chromStart (transcription end for -ve strand genes) would be non-inclusive or otherwise.

Answer 1

[Pierre Lindenbaum]

the 0-based indexing works regardless of the strand.

chr1 0 10 +

is 10 bases, starts at 0-based-including 0 and ends at 0-based-including 9

chr1 0 10 -

is 10 bases, starts at 0-based-including 9 and ends at 0-based-including 0

[GG]

I see! Thank you very much :) That was very helpful!