I was wondering if anyone has a solution to prevent bowtie2 from reverse complimenting reads. I am mapping paired-end reads using the instructions given in BSseeker2 Q&A:
Antisense.py -i mate_1.fq -o mate_1.anti.fq
bs_seeker-align.py -i mate_1.anti.fq -o mate_1.bam
bs_seeker-align.py -i mate_2.fq -o mate_2.bam
bowtie2 will map the reverse compliment of reads to the negative strand when it can't find a match. This is introducing a lot of 'methylated' cytosine noise when I view in IGV. I wrote a python script to filter out unconverted reads in my fastq files, but I can't filter out 5mC noise introduced by bowtie2's reverse compliment function. I use the flag: --bt2--norc, but this is not working at all. I think it is because that flag is exclusively used for single-end reads.
I know I can -XS flag sequences that have a specified amount of C's, but does anyone know how to prevent paired-end read reverse compliment and subsequent alignment to the negative strand?
I was wondering if anyone has a solution to prevent bowtie2 from reverse complimenting reads. I am mapping paired-end reads using the instructions given in BSseeker2 Q&A: Antisense.py -i mate_1.fq -o mate_1.anti.fq
bs_seeker-align.py -i mate_1.anti.fq -o mate_1.bam bs_seeker-align.py -i mate_2.fq -o mate_2.bam
bowtie2 will map the reverse compliment of reads to the negative strand when it can't find a match. This is introducing a lot of 'methylated' cytosine noise when I view in IGV. I wrote a python script to filter out unconverted reads in my fastq files, but I can't filter out 5mC noise introduced by bowtie2's reverse compliment function. I use the flag: --bt2--norc, but this is not working at all. I think it is because that flag is exclusively used for single-end reads.
I know I can -XS flag sequences that have a specified amount of C's, but does anyone know how to prevent paired-end read reverse compliment and subsequent alignment to the negative strand?