首先,您需要有全外显子测序的FASTQ格式数据。这通常由测序设备产生。 AI检测代码解析 # 假设您的数据已经在当前目录下,并且文件名为 sample_R1.fastq 和 sample_R2.fastq ls -lh *.fastq # 显示当前目录下的FASTQ文件信息 1. 2. 3. 2. 变异检测 可以使用GATK(Genome Analysis Toolkit)或FreeBayes等工具进...
metaspades.py –t 8 -k 21,33,55,77,99,127 --careful --pe1-1 R1.fastq --pe-2 R2.fastq -o spades_output 1. 主要参数说明: -k :k-mer的设置数,如果有多个数,中间要以逗号隔开,必须是奇数且最大设置数为127 –pe-2 和–pe1-1:输入双端序列fq文件 -t :CPU线程数 –careful:减少不匹...
drop_na(fastq_R1, fastq_R2, dcc) meta_with_files %>% count(`library name`) %>% count(n) meta_with_files %>% count(title) %>% count(n) meta_with_files %>% clipr::write_clip() used_fastq <- meta_with_files %>% select(fastq_R1, fastq_R2) %>% pivot_longer( cols = ever...
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Fastq reads were aligned using bowtie2 mm10 genome on Galaxy platform. MACS2 was used for peak calling using default parameters (FDR = 0.05). Bamcoverage was used to generate bigwig files. The BED file from the MACS2 callpeak analysis was used to perform the GO analysis using GREAT.43 ...
cerevisiae rRNA sequences with bowtie2 v 2.4.2 and only the reads that do not align were kept: bowtie2 -p8 -t -x ‘<ref_file_path>‘ -q infile.fastq.gz’ --un ‘<outfile_path>/outfile.fastq’ -S /dev/null 2> ‘<outfile_path>/Bowtie2_report.txt’. The remaining rRNA ...
Pulmonary arterial hypertension (PAH) is a progressive disease in which pulmonary arterial (PA) endothelial cell (EC) dysfunction is associated with unrepaired DNA damage. BMPR2 is the most common genetic cause of PAH. We report that human PAEC with redu
从上述的图中,以Q30为阈值,可以看出,Forward(R1)的整体质量都还可以;Reverse(R2)的测序质量稍低,平均来看,大概也在200bp左右出现了下降。 设置过滤后文件保存的位置 此示例中,是在原来path保存的目录下面,建立一个“filtered”的文件夹,用来保存过滤后的序列文件,文件名按照sample_F_filt.fastq.gz的模式命名,其中...
fastp -i CER3_1_R1.fastq.gz -I CER3_1_R2.fastq.gz -o CER3_1_R1.clean.fastq.gz -O CER3_1_R2.clean.fastq.gz -j CER3_1.json -h CER3_1.html -w 2 & #-i -I表示两个双端文件,-o -O表示输出文件,-j .json的报告,-h 网页版报告文件,-w线程数 ...
软件对测序仪下机数据进行数据转换拆分、fastq质控、比对参考基因组、Bam文件排序、Bam文件去重复、点突变和插入缺失分析、肿瘤突变负荷分析、融合分析、质控信息汇总等分析处理,检测目标肿瘤样本的基因突变情况。通过对测序数据进行分析,分析...