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...
D91N, A125E, R264W and G382R displayed even further reduced interaction with Chp1. Interestingly, mutants F98C and M102V, which are changes buried within the switch II helix of the GTPase domain important for nucleotide interactions, showed a ...
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我们拿到原始数据之后首先做数据的质控过滤,常用的软件包括fastp、fastqc。 首先使用fastqc得到网页版的质量报告,再使用trim_galore去除质量低的和接头序列,trim_galore可以指定接头序列也可以自主查询,还可以通过--length设定长度的阈值,小于该阈值的序列会被扔掉 fastqc -t 2 CER3_1_R1.fastq.gz CER3_1_R2.fastq...
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...
(1)velveth的输入默认是fasta格式的序列文件,也能识别fastq、fasta.gz、fastq.gz、sam、bam、eland和gerald文件。序列类型默认是short,也可以是shortPaired、short2、shortPaired2、long或longPaired。 命令格式为: $ ./velveth output_directory hash_length [[-file_format][-read_type] filename] 例如: ...
r2:/disk/public/test/data/ENCFF820PVO.fastq.gz heart_rep2: r1:/disk/public/test/data/ENCFF823XXU.fastq.gzr2:/disk/public/test/data/ENCFF518FYP.fastq.gz配置文件采用 yaml 格式, 这是一种简单的格式。YAML 语言教程: /blog/2016/07/yaml.html...
fastqc -o ./ -t 1 /public/home/zyhu/hfd/${i}_R1_001.fastq.gz /public/home/zyhu/hfd/${i}_R2_001.fastq.gz#检测测序文件质量 multiqc ./#合并结果文件,公众号:科研部 6、Trimmomatic去除低质量的reads: java -jar \$EBROOTTRIMMOMATIC/trimmomatic...
fastq "^1.6.0" "@react-native-community/cli-clean@^9.0.0-alpha.3": version "9.0.0-alpha.3" resolved "https://registry.yarnpkg.com/@react-native-community/cli-clean/-/cli-clean-9.0.0-alpha.3.tgz#d3cbd491c40cb23d933a221ed8e2481cb42efdda" integrity sha512-djo73BdQ+O+KhsPGwfT9...
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