
CUTADAPT . READTHEDOCS . IO {
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Title:
Recipes — Cutadapt 5.1 documentation
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Keywords {🔍}
cutadapt, reads, adapter, sequence, primer, output, read, pairedend, files, file, option, sequencing, trim, fastq, adapters, samplelrfastqgz, untrimmed, trimming, fasta, run, outfastqgz, infastqgz, pairs, bases, forward, reverse, input, data, loop, options, inputfastqgz, command, remove, polya, number, properly, rrbs, short, linked, removed, discarduntrimmed, long, trimmed, amplicon, check, paired, single, filtered, json, report,
Topics {✒️}
piping paired-end data random tag/molecular identifier paired-end files named limiting wall-clock time synchronized paired-end reads double-stranded dna fragment filtering paired-end reads option --discard-untrimmed throws nnnccg-adapter-3' 3'-adapter-gccnnn untrimmed-paired-output option short-paired-output=tooshort paired-end data ttaaggcc --untrimmed-output=untrimmed paired-end reads properly paired reads rescuing single reads improperly paired reads original methylation information single-end files reverse-complementary strand single-end reads rcfwdprimer --discard-untrimmed force fasta output restriction enzyme mspi mspi restriction sites missing base positions full dna fragment create named pipes reverse-complemented properly formatted check separate output files mismatching read ids trimmed-${r2} ${r1} ${r2} ^revprimer --discard-untrimmed ^revprimer --discard-untrimmed filtered bisulfite sequencing untrimmed-output option single sequence processing jq quickly test short-output=tooshort /dev/null input adapter separating trimmed cutadapt [options] --interleaved correct linked adapter cutadapt --fasta input trimmed read pairs rrbs library preparation poly-a-trimming filtered read pairs reverse primer
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