Originally posted by dpryan
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Besides, I think cutadaptor could to Qualitytrimming, pls see help
Additional modifications to the reads:
-q CUTOFF, --quality-cutoff=CUTOFF
Trim low-quality ends from reads before adapter
removal. The algorithm is the same as the one used by
BWA (Subtract CUTOFF from all qualities; compute
partial sums from all indices to the end of the
sequence; cut sequence at the index at which the sum
is minimal) (default: 0)
--quality-base=QUALITY_BASE
Assume that quality values are encoded as
ascii(quality + QUALITY_BASE). The default (33) is
usually correct, except for reads produced by some
versions of the Illumina pipeline, where this should
be set to 64. (default: 33)
-x PREFIX, --prefix=PREFIX
Add this prefix to read names
-y SUFFIX, --suffix=SUFFIX
Add this suffix to read names
--strip-suffix=STRIP_SUFFIX
Remove this suffix from read names if present. Can be
given multiple times.
-c, --colorspace Colorspace mode: Also trim the color that is adjacent
to the found adapter.
-d, --double-encode
When in color space, double-encode colors (map
0,1,2,3,4 to A,C,G,T,N).
-t, --trim-primer When in color space, trim primer base and the first
color (which is the transition to the first
nucleotide)
--strip-f3 For color space: Strip the _F3 suffix of read names
--maq, --bwa MAQ- and BWA-compatible color space output. This
enables -c, -d, -t, --strip-f3, -y '/1' and -z.
--length-tag=TAG Search for TAG followed by a decimal number in the
name of the read (description/comment field of the
FASTA or FASTQ file). Replace the decimal number with
the correct length of the trimmed read. For example,
use --length-tag 'length=' to correct fields like
'length=123'.
-z, --zero-cap Change negative quality values to zero (workaround to
avoid segmentation faults in old BWA versions)
So is that -q set to 5?
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