Hi,
Could somebody help me in understanding this,
In my pair-end data (raw fastq), i found some sequences with bad QC Filter Flag (Where N:Y indicates Good:Bad)
cat R1.fastq | grep :Y | wc -l
701834
cat R2.fastq | grep :Y | wc -l
701834
@HWI-1KL114:350CGTACXX:4:1101:2523:1980 1:Y:0:CGATGT
@HWI-1KL114:350CGTACXX:4:1101:6456:1995 1:Y:0:CGATGT
How do i remove these ?
I tried using fastx_toolkit
fastq_quality_filter -i R1.fastq -o Test_R1.fastq
It gives me error:
fastq_quality_filter: Invalid quality score value (char '#' ord 35 quality value -29) on line 80
@HWI-1KL114:350CGTACXX:5:1101:1983:1985 2:N:0:TGACCA
CTGGCTTCTTACTCCGTTCAGTCTGAGCTTGGAGATTATAACCCGGGAAC
+
=B@DDEFDFH>DFEIJEHFGHCHHG@H@FH9ECGCFFEAFFD?DHG#### [Line 80]
Could somebody please help me with this.
Thank you for your help in advance !
regards
CN
Could somebody help me in understanding this,
In my pair-end data (raw fastq), i found some sequences with bad QC Filter Flag (Where N:Y indicates Good:Bad)
cat R1.fastq | grep :Y | wc -l
701834
cat R2.fastq | grep :Y | wc -l
701834
@HWI-1KL114:350CGTACXX:4:1101:2523:1980 1:Y:0:CGATGT
@HWI-1KL114:350CGTACXX:4:1101:6456:1995 1:Y:0:CGATGT
How do i remove these ?
I tried using fastx_toolkit
fastq_quality_filter -i R1.fastq -o Test_R1.fastq
It gives me error:
fastq_quality_filter: Invalid quality score value (char '#' ord 35 quality value -29) on line 80
@HWI-1KL114:350CGTACXX:5:1101:1983:1985 2:N:0:TGACCA
CTGGCTTCTTACTCCGTTCAGTCTGAGCTTGGAGATTATAACCCGGGAAC
+
=B@DDEFDFH>DFEIJEHFGHCHHG@H@FH9ECGCFFEAFFD?DHG#### [Line 80]
Could somebody please help me with this.
Thank you for your help in advance !
regards
CN
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