How to filter fastq paired-end reads based on Per Tile Sequence Quality

Question

[bio_d]

Hi,

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!!

[finswimmer]

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.

Thanks!

fin swimmer

[bio_d]

https://imgur.com/5MlTmd4
https://imgur.com/18OMkf7

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.

PASS    Basic Statistics        lib200_lane7_contamination_free_tile.1.fq.gz
PASS    Per base sequence quality       lib200_lane7_contamination_free_tile.1.fq.gz
FAIL    Per tile sequence quality       lib200_lane7_contamination_free_tile.1.fq.gz
PASS    Per sequence quality scores     lib200_lane7_contamination_free_tile.1.fq.gz
PASS    Per base sequence content       lib200_lane7_contamination_free_tile.1.fq.gz
WARN    Per sequence GC content lib200_lane7_contamination_free_tile.1.fq.gz
PASS    Per base N content      lib200_lane7_contamination_free_tile.1.fq.gz
WARN    Sequence Length Distribution    lib200_lane7_contamination_free_tile.1.fq.gz
PASS    Sequence Duplication Levels     lib200_lane7_contamination_free_tile.1.fq.gz
PASS    Overrepresented sequences       lib200_lane7_contamination_free_tile.1.fq.gz
PASS    Adapter Content lib200_lane7_contamination_free_tile.1.fq.gz

PASS    Basic Statistics        lib200_lane7_contamination_free_tile.2.fq.gz
PASS    Per base sequence quality       lib200_lane7_contamination_free_tile.2.fq.gz
FAIL    Per tile sequence quality       lib200_lane7_contamination_free_tile.2.fq.gz
PASS    Per sequence quality scores     lib200_lane7_contamination_free_tile.2.fq.gz
PASS    Per base sequence content       lib200_lane7_contamination_free_tile.2.fq.gz
WARN    Per sequence GC content lib200_lane7_contamination_free_tile.2.fq.gz
PASS    Per base N content      lib200_lane7_contamination_free_tile.2.fq.gz
WARN    Sequence Length Distribution    lib200_lane7_contamination_free_tile.2.fq.gz
PASS    Sequence Duplication Levels     lib200_lane7_contamination_free_tile.2.fq.gz
PASS    Overrepresented sequences       lib200_lane7_contamination_free_tile.2.fq.gz
PASS    Adapter Content lib200_lane7_contamination_free_tile.2.fq.gz

[svp]

Any updates for this question

[gubrins]

I'm also interested!!