修剪低质量碱基，默认phred quality + 33；使用64时，需加参数：--quality-base=64 -q [5'CUTOFF,]3'CUTOFF, --quality-cutoff=[5'CUTOFF,]3'CUTOFF Quality trimming of reads using two-color chemistry (NextSeq)Quality trimming algorithm 一段序列质量编码如下：42, 40, 26, 27, 8, 7,...
参考文献：cutadapt.readthedocs.io...jianshu.com/p/412e55040...Xiao, Q., Huang, X., Zhang, Y. et al. The landscape of promoter-centred RNA–DNA interactions in rice. Nat. Plants 8, 157–170 (2022).
cutadapt [-a|-b|-g] input_reads.[fasta|fastq] > output_reads.[fasta|fastq]-a 移除reads 3‘接头序列 -g 移除reads 5‘接头序列 -e 最⼤允许的错误率 -m 除去⼩于⼀定数值的序列 -M 除去⼤于⼀定长度的序列 -q reads移去接头之前，3‘或5‘末端质量截取 ...
一、软件安装使用conda安装 conda install trim-galore 二、trim-galore的用法安装完成以后,可以使用trim_galore -help来查看软件的帮助文档...--phred33::选择-phred33或者-phred64,表示测序平台使用的Phred quality score。...$i.txt 2>&1 & ) done 命令参数解读: -q 25 # 设定Phred quality score阈值...
[login TESTA01]$ less -S 2_cleandata/A01_summary1.xls SampleID Lib ReadsCount BasesCount(bp) N(%) GC(%) Q20(%) Q30(%) A01 SPE 218500 32775000 0.00103 50.00 96.38 91.52 生信分析 QXPLUS本人目前从事生信分析相关领域, 记录一些常见的坑,也希望能帮助到类似经历的人。
cutadapt -q 5 -Q 15,20 -o out.1.fastq -p out.2.fastq in.1.fastq in.2.fastq To disable quality-trimming of R2, use -Q 0. By default, quality values are assumed to be encoded as ascii(phred quality + 33). Nowadays, this should always be the case. Some old Illumina FASTQ fi...
cutadapt --interleaved -q 20 -a ACGT -A TGCA -o trimmed.fastq reads.fastq In the following example, the input reads.fastq is interleaved, but output is written to two files trimmed.1.fastq and trimmed.2.fastq: cutadapt --interleaved -q 20 -a ACGT -A TGCA -o trimmed.1.fastq -p ...