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How to remove repeats on galaxy

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

alignment repeats galaxy
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updated by Biostar Biostar • written by pt.taklifi pt.taklifi

Hi, do you mean specific elements or just repetitive regions where reads will not uniquely map in general? If you want to remove multimappers then filtering for a MAPQ using samtools view (the -q option) might do the trick very easily.

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written by ATpoint ATpoint

install bowtie2 as admin and check if these options are available under advanced options.

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written by cpad0112 cpad0112

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