whole genome sequencing data analysis

Question

[ipb727258]

hello,

I checked the raw data by FASTQC and found red color: Per base sequence content,

Orange :per tiles sequence quality,

orange : per sequence duplication level,

do I need to do filtering or trimming? do I need to remove reads duplication?

kind response guys

[GenoMax]

Please add images using these directions: How to add images to a Biostars post

[ATpoint]

As you give no details my comment is general, and I assume this is a WGS sample. If no adapter content is flagged by fastqc you generally do not need to trim anything. Duplicates are commonly removed after alignment, e.g. using samtools fixmate/markdup, Picard MarkDuplicates, samblaster or sambamba. Alternatively they can be removed prior to alignment e.g. bbduk.sh from BBMap suite. For a more elaborate answer you need to add some details.