Question: How to filter fastq paired-end reads based on Per Tile Sequence Quality
2
gravatar for bio_d
23 months ago by
bio_d20
bio_d20 wrote:

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!!

fastqc sequencing • 1.1k views
ADD COMMENTlink written 23 months ago by bio_d20

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

ADD REPLYlink written 23 months ago by finswimmer14k

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
ADD REPLYlink modified 23 months ago • written 23 months ago by bio_d20
Any updates for this question
ADD REPLYlink written 13 months ago by svp420

I'm also interested!!

ADD REPLYlink written 3 months ago by gubrins70
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