Hi everyone,

I am trying to align paired-end reads concordantly within 600bp distance to artificial chromosomes that we created. Here is the command:

bowtie2 -p 16 -X 600 --no-mixed --very-sensitive-local -x [reference]  -1 [read1.fastq] -2 [read2.fastq] | samtools view -hbuS - | samtools sort - > output.bam

After this step, I also removed all unmapped reads using:

samtools view -h  -@ 16 -b -h -F 4 [input.bam] | samtools view -h -o  output.bam; done

Reads were able to aligned concordantly but not within the distance that I specified. For example:

SRR14646293.1027485 83  chr3_art    8823    2   2S4M1I142M1S    =
SRR14646293.1027485 163 chr3_art    198324  2   55S95M  =
SRR14646293.15739600    83  chr1_art    45200   11  2S148M  =
SRR14646293.15739600    163 chr10_art   6132    2   66S84M  =

Is there a way to force the alignment of reads within the distance I want? Thank you!