Question: miRDeep2: mapping produced bowtie.log and mapper.log - which one to trust?
0
gravatar for CandiceChuDVM
2.2 years ago by
CandiceChuDVM1.8k
United States/College Station/Texas A&M University
CandiceChuDVM1.8k wrote:

I am using miRDeep2 to analyze small RNA-Seq data.
When running mapper.pl, two log files were produced in the system: bowtie.log and mapper.log.

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.

The 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)

However, the Mapping statistics of mapper.log shows:

 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

In the 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?

ADD COMMENTlink written 2.2 years ago by CandiceChuDVM1.8k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2502 users visited in the last hour