what is the gap column of GMAP output

[gruberjd]

Hello all--

Really simple, I hope simple to answer, question. What is the gap column in GMAP output? What do the codes mean? For example:

'M998 D1 M41 I1 M1506'

I've looked at the original publication, done Googling and searching SA, and I just don't see any explanation for what this means (maybe I missed it somewhere?). Can someone quickly bring me up to speed?

Thanks!
J

[Joshua_HIT]

I think it means operations applied to finish the Mapping procedue, "M" means Match, "D"means Delete,"I" means insert, and so on.

I am using GMAP these days, but I did not reviece a result like this....mine is M123D3I23.... (I set the output formate samse).

but I have a question that: why the output of GMAP can only be printed on terminal?? I don't know why? Do I have to using | tee Document.sam to copy the output into a file?

[gruberjd]

joshua -- thanks for the answer. I think I'll have to sit down with a result to see what is being deleted, matched, etc to fully understand.

yes, i think you are right that you have to pipe the output. I generally use '>' but '| tee filename' as you said is equivalent. I wouldn't use .sam though, it is not at all similar to samtools format, is it? Maybe that's a format -f that I don't use.... I prefer '-f 3' to get a nice tab-delimited structure.

thanks for replying!