SEQanswers

Go Back   SEQanswers > Applications Forums > Metagenomics



Similar Threads
Thread Thread Starter Forum Replies Last Post
how to get the count of reads mapped to rRNA regions? bvk RNA Sequencing 22 04-20-2016 06:15 AM
Count intervals of multiply mapped reads overlapping the genome sunkissbean Bioinformatics 2 01-08-2015 06:58 AM
What is wrong with merely 28% tophat2 mapped reads are counted by HTSeq-count bbl Bioinformatics 3 06-19-2014 10:00 AM
HTSeq-count large proportion of mapped reads with no_feature edm1 Bioinformatics 4 05-26-2014 08:28 AM

Reply
 
Thread Tools
Old 04-20-2017, 02:06 AM   #1
GUZUMO
Junior Member
 
Location: China

Join Date: Nov 2016
Posts: 4
Default how to count the mapped reads with bbmap?

hello, I have assembled paired reads with Megahit, and now I want to know how many reads are uesd to make up those contigs(reads%).
I have tried bbmap and find this in STR:
Pairing data: pct reads num reads pct bases num bases

mated pairs: 36.1655% 52614378 37.2210% 15687793904
bad pairs: 2.9658% 4314738 3.0270% 1275797796
insert size avg: 338.64


Read 1 data: pct reads num reads pct bases num bases

mapped: 46.8503% 68158783 46.8339% 10145704082
unambiguous: 46.3132% 67377420 46.2987% 10029749277
ambiguous: 0.5371% 781363 0.5353% 115954805
low-Q discards: 0.0000% 0 0.0000% 0

perfect best site: 18.9679% 27594901 19.0008% 4116175782
semiperfect site: 21.5567% 31361110 21.5960% 4678380777
rescued: 0.7859% 1143367

Match Rate: NA NA 95.8928% 9735647890
Error Rate: 41.6441% 36902108 2.0807% 211247627
Sub Rate: 41.6137% 36875119 1.9638% 199375874
Del Rate: 0.7019% 622010 0.0682% 6927772
Ins Rate: 0.8580% 760297 0.0487% 4943981
N Rate: 6.7397% 5972234 2.0264% 205736337
(read2 data omitted)
Average coverage: 305.47
Standard deviation: 902.02
Percent scaffolds with any coverage: 100.00
Percent of reference bases covered: 99.95

And I wonder what does this means?
How to calculate the reads% mapped to contigs?
Thanks.
(new to this ,question may be stupid but I have no idea about this.)
GUZUMO is offline   Reply With Quote
Old 04-20-2017, 06:00 AM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,439
Default

Just to clarify. You took the original reads and then mapped them back to the assembly done with MegaHit using BBMap?
GenoMax is offline   Reply With Quote
Old 04-20-2017, 06:09 PM   #3
GUZUMO
Junior Member
 
Location: China

Join Date: Nov 2016
Posts: 4
Default

yes,is there something wrong?
thx
GUZUMO is offline   Reply With Quote
Old 04-24-2017, 10:20 AM   #4
Brian Bushnell
Super Moderator
 
Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,668
Default

For paired reads, you can find the total percent mapped by adding the read 1 percent (where it says "mapped: 46.8503%") and read 2 percent, then dividing by 2. The different columns tell you the count/percent of each event. For example, for the "num bases" column and "sub rate" row, the entry indicates there were 199375874 base substitutions (mismatches) compared to the reference, for read 1.
Brian Bushnell is offline   Reply With Quote
Old 04-25-2017, 03:09 AM   #5
GUZUMO
Junior Member
 
Location: China

Join Date: Nov 2016
Posts: 4
Default

Thanks,
So how to understand "Match Rate" and "Error Rate"?
is there a pdf or something that explain the result of bbmap?
GUZUMO is offline   Reply With Quote
Old 04-25-2017, 11:54 AM   #6
Brian Bushnell
Super Moderator
 
Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,668
Default

Considering the cigar strings from alignment, "Match Rate" is the number of symbols indicating a reference match (=) and error rate is the number indicating substitution, insertion, or deletion (X, I, D).

BBMap does not have a PDF, but its documentation is included in /bbmap/docs/guides/BBMapGuide.txt
Brian Bushnell is offline   Reply With Quote
Reply

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 01:47 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO