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7 hours ago by

hello everyone ,

I am analyzing fastq files on galaxy. I aligned fastq files to hg38 reference genome using bowtie2 and produced BAM files. now I want to remove alpha satellite repeats, Alu repeats, ribosomal DNA repeats, and other repeat regions. I think -k 1 -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 -X 2000 –rg-id options in bowtie2 removes these repeats however I'm not sure how to do this task on galaxy

I would appreciate your help



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