conda install -c bioconda fastqc -y #fastqc --help conda install -c bioconda -c conda-forge multiqc #pip install multiqc conda install -c bioconda fastp -y #https://www.jianshu.com/p/10d8daa57d1d conda install -c bioconda fastx_toolkit -y #/home/hucy/anaconda3/envs/SNPseq/bin/fa...
并添加读取组信息 FastqToSam函数的文档: Tool documentation 官方示例: java -Xmx8G -jar picard.jar FastqToSam \ #目前该函数已经集成在conda...samtools faidx ref.fasta # 环境中应自己安装samtools,该函数未集成于GATK 这会生成一个名为 ref.fasta.fai 的文本文件,其中每个 FASTA 重叠群每行一条记录....
>conda install -c bioconda package_name Packages can be updated with: >conda update package_name In general, because conda only performs the smallest set of updates in order to satisfy the dependency graph, it isstrongly advisedto always update the environment as a whole afterwards: ...
python RTDmaker.py ShortReads --assemblies </path/to/assembly-folder> --references </path/to/references-folder> --SJ-data </path/to/SJ-folder> --SJ-reads <2,1> --genome <genome.fasta> --fastq </path/to/fastq-folder> --tpm <1, 1> --fragment-len <0.7> --antisense-len <0.5>...
fastq converts a BAM to a FASTQ fasta converts a BAM to a FASTA -- Statistics bedcov read depth per BED region depth compute the depth flagstat simple stats idxstats BAM index stats phase phase heterozygotes stats generate stats (former bamcheck) -- Viewing flags explain BAM flags tview ...