Issue with Bowtie2 mapping
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?
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...can you show the summary report of trimmomatic? Probably a lot got trimmed away/discarded.
i used clean reads to reference mapping, discarded reads by Trimmomatic deposited into D1R1U.fastq and D1R2U.fastq and were ignored from downstream acts.
Ok my bad. How did you count the reads in the fastq files?
Based on FastQC report, each cleaned files (for. and rev.) have 201720569 but Bowtie2 used 98031099 reads to mapping
I would verify this e.g. by
awk '{s++}END{print s/4}' file_cleaded.fastqto be sure.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.
Unlikely, we're talking about two of the most established and widely used bioinformatic tools out there.