Log.final.output

[GoogleCodeExporter]

What steps will reproduce the problem?
1. input: paired-end read
2. Log.final.out 

What is the expected output? 
statistics for both paired-end reads
read1:  188881802
read2:  188881802

What do you see instead?
just for one single file ??

e.g.
                          Number of input reads |   188881802
                      Average input read length |   102
                                    UNIQUE READS:
                   Uniquely mapped reads number |   159058244
                        Uniquely mapped reads % |   84.21%

however Aligned.out.sam has both ends reads mapped:

418527540 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
379423218 + 0 mapped (90.66%:-nan%)
418527540 + 0 paired in sequencing
209249304 + 0 read1
209278236 + 0 read2
379423218 + 0 properly paired (90.66%:-nan%)
379423218 + 0 with itself and mate mapped

What version of the product are you using? On what operating system?
STAR 2.3 
Linux tbi-pbs1 2.6.37.6-0.20-default #1 SMP 2011-12-19 23:39:38 +0100 x86_64 
x86_64 x86_64 GNU/Linux

Please provide any additional information below.

any comments would be appreciated very much!

Original issue reported on code.google.com by vkurys...@yahoo.com on 25 Feb 2013 at 7:50

[GoogleCodeExporter]

When calculating the statistics in the Log.final.out, STAR considers both mates 
of a paired-end read as one read. By default, STAR only outputs correctly 
paired alignments. I think this should explain your observations.
If you have further questions, please post them at 
https://groups.google.com/forum/#!forum/rna-star
or email me at dobin@cshl.edu

Original comment by adobin@gmail.com on 25 Feb 2013 at 8:33

• Changed state: Accepted
• Added labels: Type-Task
• Removed labels: Type-Defect

[GoogleCodeExporter]

now it's clear. thank you.
however it's not obvious from the description of output..

Original comment by vkurys...@yahoo.com on 26 Feb 2013 at 3:05