’–pre-trim-phred’ trim based on phred quality value to deal with higher error rates towards the end of reads.For example, to trim 5 bases at the right side of reads: –pre-trim-right 5 ’–pre-trim-right’ trim a fixed number of bases at right read end.For example, to trim 5 bases at the left side of reads: –pre-trim-left 5 ’–pre-trim-left’ trim a fixed number of bases at left read end.The value will _1.fastq.gz and _2.fastq.gz for read 1 and read 2 respectively ’–target’ a base path for the output files.’–reads2’ define the path to the read 2 FASTQ file of reads.’–reads’ define the path to the read 1 FASTQ file of reads.’–adapters’ define the path to the adapter FASTA file to trim.’–zip-output GZ’ the input FASTQ files are gzipped so we will output gzipped FASTQ to save space.’–min-read-length’ the minimum read length allowed after trimming is 25bp.’–max-uncalled 300’ allows as many as 300 uncalled or N bases (MiSeq read lengths can be 300bp).’–adapter-trim-end RIGHT’ uses a trimming strategy to remove the adapter from the 3 prime or RIGHT end of the read. ’–adapter-min-overlap 7’ requires a minimum of 7 bases to match the adapter.
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