cutadapt -b file:$Linker_file -n 14 --no-indels -o $OUTPUT_DIRECTORY/$OUTPUT_PREFIX.noLinker --info-file $OUTPUT_DIRECTORY/$OUTPUT_PREFIX.Linker_info --discard -O 18 $OUTPUT_DIRECTORY/$OUTPUT_PREFIX.fastq > $OUTPUT_DIRECTORY/$OUTPUT_PREFIX.stat & 目的是识别$OUTPUT_DIRECTORY/$OUTPUT_PREFI...
Wildcards 使用N，Y，T这种通配符 Repeated bases in the adapter sequence 可以去除ploy-A AAAAAAAAAA )等价于 A{10} 对reads的修剪 Removing a fixed number of bases #移除一定数目碱基 -u LENGTH, --cut=LENGTH #修剪reads 5'/3' 碱基，正数表示从 5'移除碱基，负数表示从3'移除碱基 Qual...
cutadapt 允许采用IUPAC 的碱基字符表 字母N代表任意碱基, 在去除barcode 序列是非常有用, 比如 ACGTANNNNNTAC 其中NNNN 代表barcode 序列, 又叫做index 序列 cutadapt -a ACGTAANNNNTTAGC -o output.fastq input.fastq 兼并引物序列:YACGT; 就是说可能为 CACGT 或者 TACGT cutadapt -a YACGT -o output.f...
cutadapt -O 1 -a AGATCGGAAGAG -A AGATCGGAAGAG -e 0.1 -q 20,20 -m 75 --max-n=0.1 -o *_clean_R1.fq -p *_clean_R2.fq *_1.fq.gz *_2.fq.gz 批量运行命令如下: cat SRR_Acc_List.txt | while read line do cutadapt -O 1 -a AGATCGGAAGAG -A AGATCGGAAGAG -e 0.1 -q ...
一.Trim Galore介绍 Trim Galore是对FastQC和Cutadapt的包装。...--phred33::选择-phred33或者-phred64,表示测序平台使用的Phred quality score。...-- trim-n : 移除read一端的reads 二.使用trim-galore去除低质量的reads和adaptor 首先,创建保存输出数据的文件夹。...Path to Cutadapt set as: 'cutadapt...
tail -n 4 input.fastq | cutadapt -a AACCGGTT - > output.fastq The tail -n 4 prints out only the last four lines of input.fastq, which are then piped into Cutadapt. Thus, Cutadapt will work only on the last read in the input file. In most cases, you should probably use - at ...
The second option is to not use the-noption, but to run Cutadapt twice, first removing one adapter and then the other. It is easiest if you use a pipe as in this example: cutadapt -g ^TTAAGGCC -g ^AAGCTTA input.fastq | cutadapt -a TACGGACT - > output.fastq ...
下面是100个lncRNA组装流程的软件的笔记教程 Trim Galore是对FastQC和Cutadapt的包装。适用于所有高通量测...
This is needed when you want to search for literal 'N' characters. Options for filtering of processed reads: --discard-trimmed, --discard Discard reads that contain the adapter instead of trimming them. Also use -O in order to avoid throwing ...
mask: Replace the adapter sequence and up- or downstream sequence with 'N' characters lowercase: Convert the adapter and up- or downstream sequence to lowercase. none: Do not change the read. The information which adapter was found is still used demultiplexing). --rc, --revcomp :ref:`Check...