【atac-single.sh】对ATAC的fq.gz文件进行一键前期处理,得到可用的bam文件,文件在最下方... 脚本流程如下: 1、【trim_galore】命令去接头 2、【bwa】进行比对 3、【samtools】进行bam转换 4、【picard】去除Duplication 5、【samtools】进行bam filter,具体参数参考脚本 6、【deeptools】进行ATAC bam shift 7、【...
If you want to create a single, interleaved FASTQ fileforpaired-end data, you can justwriteboth to /dev/stdout: bedtools bamtofastq -i x.bam -fq /dev/stdout -fq2 /dev/stdout > x.ilv.fq 直接转换成fastq 例如可以: bamToFastq -iunmapped.bam-fq unmapped.fastq AI代码助手复制代码 如果需...
--merged_out in the merging mode, specify the file name to store merged output, or specify --stdout to stream the merged output (string [=]) --include_unmerged in the merging mode, write the unmerged or unpaired reads to the file specified by --merge. Disabled by default. -6, --phr...
qrqc:提供了用于快速读取FASTQ文件和质量控制报告的工具。 Rsamtools:主要用来读取、写入并处理SAM/BAM文件,同样可以处理相关联的FASTQ文件。 这些工具包各具特色,通用的处理方法包括序列质量评估、读取和过滤等,帮助用户实现对大规模测序数据的高效处理。 四、实战应用案例 在处理FASTQ文件时,ShortRead等包使得用户能够进...
to the files specified by --out1 and --out2. The merging mode is disabled by default. --merged_out in the merging mode, specify the file name to store merged output, or specify --stdout to stream the merged output (string [=]) --include_unmerged in the merging mode, write the ...
"ehbio.bam" may be a binary file. See it anyway? 1. 2. 小白:“哎呀,错了,应该这样。” 嗒嗒嗒敲键盘。 $ samtools view ehbio.bam # 回车一敲,灾难,电脑要卡死,赶紧按`control + c` $ samtools view ehbio.bam | less # 这下终于可以查看了 ...
bamtofastq [options] [bam-path][output-path] Replace [bam-path] with the path to the input BAM, [output-path] with the path to the output directory, and include any relevant [options] (listed below). For example, if your BAM file is located at /path/to/mydata.bam, you want ...
8 --dta -x /path/to/file/hg19/genome -1 ${i}_out_R1.fastq.gz -2 ${i}_out_R2.fastq.gz -S ${i}.sam & done 4. 排序 for i inls *.sam; do i=${i/.sam/}; nohup samtools sort -@ 8 -o ${i}.bam ${i}.sam & done ...
老板:“先查看一下bam文件内容。” 小白:嗒嗒嗒敲键盘。 $ less ehbio.bam "ehbio.bam" may be a binaryfile. See it anyway? 小白:“哎呀,错了,应该这样。” 嗒嗒嗒敲键盘。 $ samtools view ehbio.bam # 回车一敲,灾难,电脑要卡死,赶紧按`control + c` ...
就面临改名的问题。比如: 代码语言:javascript 代码运行次数:0 运行 AI代码解释 touch{A..X}_S1_L001_R1_001.fastq.gz{A..X}_S1_L001_R2_001.fastq.gz ls*gz|cat|headA_S1_L001_R1_001.fastq.gzA_S1_L001_R2_001.fastq.gzB_S1_L001_R1_001.fastq.gzB_S1_L001_R2_001.fastq.gzC_S1_L001...