Question: The Score Meaning Of Output (.Maf) Using Mugsy And Get A Overall Aligned Score
gravatar for a81526a
6.4 years ago by
a81526a60 wrote:

Well, I'm a newbie of Mugsy, so...hope I'm not asking a stupid question....

I've already have a set of contigs which is done by de novo assembler. Format of these contigs is fasta. Now I want to align these contigs to a reference sequence by using Mugsy. And obtain only single score shown the similarity between contigs and reference sequence.

[H24991180@node03 r2]$ mugsy --directory /home/H24991180/Mugsy/Velvet/r2 --prefix velvet_r2 contigs.fa

Parsing sequences for contigs num_seqs:51179

Parsing sequences for Arabidosis_thaliana num_seqs:5

2 genomes

Starting Nucmer: Sun Sep 22 01:14:14 CST 2013 . Finished Nucmer Sun Sep 22 01:51:51 CST 2013

Starting MUGSYWGA: Sun Sep 22 01:51:51 CST 2013

Finished MUGSYWGA: Sun Sep 22 05:49:26 CST 2013

Final output (MAF format): /home/H24991180/Mugsy/Velvet/r2/velvet_r2.maf

Finished Sun Sep 22 05:49:26 CST 2013

The output of maf file:

maf version=1 scoring=mugsy

a score=43769 label=1 mult=2

s|332002898|gb|CP002688.1| 23544873 37605 + 26975502

s contigs.NODE_203395_length_51126_cov_11.976137 5065 40426 - 51218

a score=32893 label=2 mult=2

s|330250293|gb|CP002685.1| 3391933 32785 + 19698289

s contigs.NODE_10073_length_33024_cov_248.175110 0 32791 + 33116


I want to know what's the meaning of "score" here ?

And because it only showed identity and score for each contig,how can I get a summarizing values representing the similarity between contigs and reference sequence.

I've searched for hours and can't seem to find a straight answer. Please do help me....thanks!!

similarity reference • 2.8k views
ADD COMMENTlink modified 6.4 years ago • written 6.4 years ago by a81526a60
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1091 users visited in the last hour