Question: How to remove repeats on galaxy
0
gravatar for pt.taklifi
17 days ago by
pt.taklifi60
pt.taklifi60 wrote:

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

galaxy repeats alignment • 65 views
ADD COMMENTlink written 17 days ago by pt.taklifi60
1

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 REPLYlink written 17 days ago by ATpoint44k
1

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

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

ADD REPLYlink written 17 days ago by GenoMax95k
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