calculate a base's distance to the read's 3' end

[lyz1030]

Hi,



Can anyone tell me how to calculate a base's distance to 3' end respectively for the forward and reverse strand read. I want to konw if the following formula is correct?



1)for forward strand read: distance=the read's alignmnet end position-the base's position

2)for reverse strand read: distance=the base's position-the read's alignment start position



Thanks

[sphil]

Hi,



Can anyone tell me how to calculate a base's distance to 3' end respectively for the forward and reverse strand read. I want to konw if the following formula is correct?



1)for forward strand read: distance=the read's alignmnet end position-the base's position

2)for reverse strand read: distance=the base's position-the read's alignment start position



Thanks

correct....IF you name the 3' end of a read (on the reverse strand) as the start of the read and not the end!

[lyz1030]

I use the bwa results as the input, so the input reads is refered to the reads from the bam file. For this kinds of reads (reverse strand), I am not sure which end is the 3' end. I don't know why the 3' end of a read (forward strand and reverse strand) can be named but not fixed.