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4.2 years ago
bio_d ▴ 20
I am having trouble filtering reads based on Per Tile Sequence Quality. The fastqc quality report suggests that my reads have issues with Per Tile Sequence Quality. I have tried filterbytile.sh script (BBMap package) but it fails to filter, in fact I lose out reads while the fastqc report post-processing with filterbytile.sh gave worse results. Please advise!!
Hello bio_d ,
could you please show us the exact command you used? Also the fastqc reports might be useful for us to help you.
filterbytile.sh -Xmx64g in1=lib200_lane7_contamination_free.1.fq.gz in2=lib200_lane7_contamination_free.2.fq.gz out1=lib200_lane7_contamination_free_tile.1.fq.gz out2=lib200_lane7_contamination_free_tile.2.fq.gz
FASTQC post filterbytile processing.
I'm also interested!!