Hi ,
I'm writing to ask some question about FastQ quality trimmer.
I have loaded Fastx toolkit on my linux machine, I want to use that tool to trim bases from the 3' and 5' and with a low quality score <28.
I have a paired end data files of 101 bases, only in the R2 file I have a decrease of quality in the 3' and in the 5' end, I attached the relative quality box plot.
How should I set the parameter reported below of Fastq quality trimmer to obtain a good quality box plot as for R1 (attached)?
fastq_quality_trimmer -h
usage: fastq_quality_trimmer [-h] [-v] [-t N] [-l N] [-z] [-i INFILE] [-o OUTFILE]
Part of FASTX Toolkit 0.0.13 by A. Gordon ([email protected])
[-h] = This helpful help screen.
[-t N] = Quality threshold - nucleotides with lower
quality will be trimmed (from the end of the sequence).
[-l N] = Minimum length - sequences shorter than this (after trimming)
will be discarded. Default = 0 = no minimum length.
[-z] = Compress output with GZIP.
[-i INFILE] = FASTQ input file. default is STDIN.
[-o OUTFILE] = FASTQ output file. default is STDOUT.
[-v] = Verbose - report number of sequences.
If [-o] is specified, report will be printed to STDOUT.
If [-o] is not specified (and output goes to STDOUT),
report will be printed to STDERR.
I will appreciate your help.
Thanks
I'm writing to ask some question about FastQ quality trimmer.
I have loaded Fastx toolkit on my linux machine, I want to use that tool to trim bases from the 3' and 5' and with a low quality score <28.
I have a paired end data files of 101 bases, only in the R2 file I have a decrease of quality in the 3' and in the 5' end, I attached the relative quality box plot.
How should I set the parameter reported below of Fastq quality trimmer to obtain a good quality box plot as for R1 (attached)?
fastq_quality_trimmer -h
usage: fastq_quality_trimmer [-h] [-v] [-t N] [-l N] [-z] [-i INFILE] [-o OUTFILE]
Part of FASTX Toolkit 0.0.13 by A. Gordon ([email protected])
[-h] = This helpful help screen.
[-t N] = Quality threshold - nucleotides with lower
quality will be trimmed (from the end of the sequence).
[-l N] = Minimum length - sequences shorter than this (after trimming)
will be discarded. Default = 0 = no minimum length.
[-z] = Compress output with GZIP.
[-i INFILE] = FASTQ input file. default is STDIN.
[-o OUTFILE] = FASTQ output file. default is STDOUT.
[-v] = Verbose - report number of sequences.
If [-o] is specified, report will be printed to STDOUT.
If [-o] is not specified (and output goes to STDOUT),
report will be printed to STDERR.
I will appreciate your help.
Thanks
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