Filter and Trim your Paired-end FastQ file

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FastQtrimmer.pl

Filter and Trim your Paired-end FastQ file

get script

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git clone https://github.com/wlz0726/SequenceMapping.git

As you get the Illumina sequencing data from a company like BGI/Novogene, first thing you (probably) need to do is to do the sequnce quality check and filter the low quality reads.

Here I assume you have no adaptor problem and the sequencing company have already remove the adaptor before hand over you the data.

FastQtrimmer.pl will trim and filtering Paired-end reads in gz format, and the following reads will be removed:

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1)  >=10% unidentified nucleotides (N)
2)  with a phred quality <=7 for >65% of the read length
3)  reads are trimmed if they had three consecutive bp with a phred quality of <=13,
    and discarded if they were shorter than 45 bp

Example:
Your have one Paired-end FastQ file named SampleID.1.fq.gz and SampleID.2.fq.gz with phred33 quality system, the read length is 100 bp,

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perl FastQtrimmer.pl SampleID.1.fq.gz SampleID.2.fq.gz SampleID.Filter 33 100

the results will be:
SampleID.Filter.1.TrimTwoSide.fq.gz
SampleID.Filter.2.TrimTwoSide.fq.gz

fastq_Phred64_to_33_gz.pl

If your reads are in Phred64 quality system, and you need to transform Phred64 reads to Phred33, run like this:

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perl fastq_Phred64_to_33_gz.pl input.1.fq.gz input.2.fq.gz OutputPrefix

After read Quality control: Map with BWA and do Indel realignment with GATK