Question: Issue with Bowtie2 mapping
0
gravatar for reza
10 months ago by
reza220
Iran
reza220 wrote:

I am working on a sets of paired end reads, in first step I trimmed them using Trimmomatic with following command

java -jar trimmomatic-0.36.jar PE 10.10B_R1.gz 10.10B_R2.gz D1R1P.fastq D1R1U.fastq D1R2P.fastq D1R2U.fastq LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:50

There are 201720569 reads in each output files (D1R1P.fastq and D1R2P.fastq). Then I mapped outputted files to reference genome using Bowtie2

bowtie2 -x reference -1 D1R1P.fastq -2 D1R2P.fastq --un-conc unmapped -S D1.sam

output of Bowtie2 say me this:

98031099 reads; of these:
  98031099 (100.00%) were paired; of these:
    10497294 (10.71%) aligned concordantly 0 times
    73271391 (74.74%) aligned concordantly exactly 1 time
    14262414 (14.55%) aligned concordantly >1 times

98.16% overall alignment rate

Why all paired reads are not including in mapping process?

ADD COMMENTlink modified 10 months ago • written 10 months ago by reza220

...can you show the summary report of trimmomatic? Probably a lot got trimmed away/discarded.

ADD REPLYlink written 10 months ago by ATpoint35k

i used clean reads to reference mapping, discarded reads by Trimmomatic deposited into D1R1U.fastq and D1R2U.fastq and were ignored from downstream acts.

ADD REPLYlink written 10 months ago by reza220

Ok my bad. How did you count the reads in the fastq files?

ADD REPLYlink written 10 months ago by ATpoint35k

Based on FastQC report, each cleaned files (for. and rev.) have 201720569 but Bowtie2 used 98031099 reads to mapping

ADD REPLYlink written 10 months ago by reza220

I would verify this e.g. by awk '{s++}END{print s/4}' file_cleaded.fastq to be sure.

ADD REPLYlink written 10 months ago by ATpoint35k

Thank you for trying to help me. i have no problem with reads number. Program in each run, show different behaviors, which I think is due to the existence of a bug.

ADD REPLYlink written 9 months ago by reza220

Unlikely, we're talking about two of the most established and widely used bioinformatic tools out there.

ADD REPLYlink written 9 months ago by ATpoint35k
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: 989 users visited in the last hour