How to remove repeats on galaxy

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3.9 years ago

pt.taklifi ▴ 60

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 • 828 views

ADD COMMENT • link updated 3.7 years ago by Biostar 20 • written 3.9 years ago by pt.taklifi ▴ 60

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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.

ADD REPLY • link 3.9 years ago by ATpoint 85k

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I'm not sure how to do this task on galaxy

Please ask on Galaxy help forum here: https://help.galaxyproject.org/

ADD REPLY • link 3.9 years ago by GenoMax 147k

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

ADD REPLY • link 3.7 years ago by cpad0112 21k

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