SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
rethinking log-log RPKM plots BAMseek RNA Sequencing 6 12-22-2011 10:44 AM
understanding dwgsim_eval output oiiio Bioinformatics 12 08-15-2011 04:10 PM
Understanding GSNAP output burt Bioinformatics 0 01-16-2011 06:06 PM
Maq output: assemble.log file contains what? soniat Bioinformatics 0 12-15-2008 06:25 AM
Understanding Qualities using MAQ binnaz Illumina/Solexa 1 11-06-2008 01:41 AM

Reply
 
Thread Tools
Old 06-28-2010, 03:43 AM   #1
anna_vt
Junior Member
 
Location: London

Join Date: Jun 2009
Posts: 5
Default Understanding Maq log output

Hi,

I have a couple of questions about my Maq map output if anyone knows the answers I'd really appreciate them:

Code:
[match_search]  98% processed in 20717.101 sec: 31618863 / 21294334 = 1.485
[match_search]  99% processed in 20765.187 sec: 28388678 / 20109661 = 1.412
[match_search] 100% processed in 20768.725 sec: 1164880 / 1048335 = 1.111
[match_core] sorting the hits and dumping the results...
[ma_load_reads] loading reads...
[ma_load_reads] 2000000*2 reads loaded.
[mapping_count_single] 7, 11, 16, 27
[maq_indel_pe] the indel detector only works with short-insert mate-pair reads.
[match_data2mapping] 1922258 out of 4000000 raw reads are mapped with 0 in pairs.
-- (total, isPE, mapped, paired) = (2000000, 0, 1922258, 0)
First, what is the "mapping_count_single" - what do these 4 numbers mean?

Second, this file contained 2,000,000 reads (8 million lines in fastq format), so how come the logfile says x out of 4000000 raw reads are mapped?

Many Thanks
Anna
anna_vt is offline   Reply With Quote
Old 10-17-2011, 07:48 PM   #2
Tally
Member
 
Location: Sydney

Join Date: Aug 2011
Posts: 12
Default

I have a similar issue. My output log reports n_reads*2 because they are paired end, but it looks like that is not the case for your data. My issue is the "x out of n raw reads are mapped" part:

[match_data2mapping] 1976956 out of 2000000 raw reads are mapped with 1969400 in pairs.
-- (total, isPE, mapped, paired) = (2000000, 1, 1976956, 1969400)

What happened to the remaining 23,044 reads? It is not that they are simply unmapped, as I have a number of unmapped reads in my .sam alignment file.

Any help much appreciated.
Tally is offline   Reply With Quote
Reply

Tags
maq map, output

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 09:42 AM.


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