SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
BLASR output - what does each column mean? ritzriya Pacific Biosciences 7 01-20-2014 09:52 PM
Unrecognized characters in the read base column of mpileup output charlie_sequencing Bioinformatics 1 11-06-2013 06:33 PM
varScan output, all N in the REF column xgong Bioinformatics 5 11-08-2012 08:37 AM
what is the fourth column in the output file of CNVnator yuhao Bioinformatics 0 07-13-2012 10:07 PM
Using Gmap output hrajasim Bioinformatics 2 06-18-2010 12:08 PM

Reply
 
Thread Tools
Old 09-11-2013, 01:14 PM   #1
gruberjd
Member
 
Location: Michigan

Join Date: Nov 2011
Posts: 13
Default what is the gap column of GMAP output

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
gruberjd is offline   Reply With Quote
Old 10-18-2013, 11:13 PM   #2
Joshua_HIT
Junior Member
 
Location: Shanghai

Join Date: Oct 2013
Posts: 8
Default

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?
Joshua_HIT is offline   Reply With Quote
Old 10-18-2013, 11:23 PM   #3
gruberjd
Member
 
Location: Michigan

Join Date: Nov 2011
Posts: 13
Default

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!
gruberjd is offline   Reply With Quote
Reply

Tags
gmap, twu

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 04:26 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO