- Trim adapters in R2 reads with cutadapt.
- cutadapt.log Cutadapt output log file.
{sample}_clean_2.fq.gz R2 reads file after trimming adapters.
Usage: CellCosmo rna cutadapt [OPTIONS]
Options:
--fq TEXT Required. R2 reads from step Barcode. [required]
--gzip Output gzipped fastq files.
--adapter-fasta TEXT Additional adapter fasta file.
--minimum-length INTEGER Discard processed reads that are shorter than
LENGTH. [default: 20]
--nextseq-trim INTEGER Quality trimming of reads using two-color
chemistry (NextSeq). Some Illumina instruments use
a two-color chemistry to encode the four bases.
This includes the NextSeq and the NovaSeq. In
those instruments, a `dark cycle` (with no
detected color) encodes a G. However, dark cycles
also occur when sequencing `falls off` the end of
the fragment. The read then contains a run of
high-quality, but incorrect `G` calls at its 3'
end. [default: 20]
--overlap INTEGER Since Cutadapt allows partial matches between the
read and the adapter sequence, short matches can
occur by chance, leading to erroneously trimmed
bases. For example, roughly 0.25 of all reads end
with a base that is identical to the first base of
the adapter. To reduce the number of falsely
trimmed bases, the alignment algorithm requires
that at least {overlap} bases match between
adapter and read. [default: 10]
--insert INTEGER Read2 insert length. [default: 150]
--cutadapt-param TEXT Other cutadapt parameters. For example,
--cutadapt_param '-g AAA'
-o, --outdir TEXT Output directory. [required]
-s, --sample TEXT Sample name. [required]
-t, --thread INTEGER Thread to use. [default: 4]
-h, --help Show this message and exit.