I am using
miRDeep2 to analyze small RNA-Seq data.
mapper.pl, two log files were produced in the system:
Before executing the
bowtie function to map reads to genome index,
mapper.pl has done (1) parsing fastq to fasta format (2) discarding sequences with non-canonical letters (3) discarding short reads (4) collapsing reads.
bowtie.log looks like below:
# reads processed: 138945 # reads with at least one reported alignment: 74938 (53.93%) # reads that failed to align: 50691 (36.48%) # reads with alignments suppressed due to -m: 13316 (9.58%) Reported 122526 alignments to 1 output stream(s)
Mapping statistics of
parsing fastq to fasta format discarding sequences with non-canonical letters discarding short reads collapsing reads mapping reads to genome index trimming unmapped nts in the 3' ends Log file for this run is in mapper_logs and called mapper.log_33416 Mapping statistics #desc total mapped unmapped %mapped %unmapped total: 11965391 11469171 496220 0.959 0.041 seq: 11965391 11469171 496220 0.959 0.041
Mapping statistics, the total column equals to the number of fastq reads in the original fastq file.
I was wondering which mapping statistics should I trust and what's the difference between these two?