但是我git下载了它源代码,发现其压缩包里面的STAR-Fusion命令本来就是可以直接使用的,无需conda来管理了。可以看到, 其实1.9的star-fusion的这个STAR-Fusion.map_chimeric_reads_to_genes 脚本内容跟前面conda自己配置的1.6版本内容不一样: 531 /home/data/fusion/STAR-Fusion-master/util/STAR-Fusion.map_chimeric_...
# trim,star 两个软件即可 conda create-n starFusion conda activate starFusion conda install-c bioconda trim-galore conda install-c bioconda star-fusion 可以看到目前两个软件版本是: 代码语言:javascript 代码运行次数:0 复制 Cloud Studio代码运行 STAR--version2.7.10aSTAR-Fusion--versionSTAR-Fusion versio...
使用安装好的conda来 安装软件的代码如下所示: # trim,star 两个软件即可 conda create -n starFusion conda activate starFusion conda install -c bioconda trim-galore conda install -c bioconda star-fusion 可以看到目前两个软件版本是: STAR --version 2.7.10a STAR-Fusion --version STAR-Fusion version...
conda install star-fusion=0.5.4 -cbioconda conda install fusion-inspector -c bioconda conda install gmap-fusion -c bioconda#出现如下报错 PackagesNotFoundError: The following packages are not available from current channels: - gmap-fusion -> perl=5.22.0 需要设置Set up channels conda config --add...
1. conda install -c bioconda star-fusion 因为需要使用 star 这个比对工具对 fastq 比对成 bam,所以那部 分请自行学习,这里我们已经得到了 bam 文件啦。 数据库文件的下载 可 以 先 去 https://data.broadinstitute.org/Trinity/CTATRESOURCELIB/ 查看 对应的参考基因组版本: 1. mkdir -p ~/biosoft/star...
运行FusionInspector工具: conda install -c bioconda fusion-inspector bin_star='~/biosoft/STAR-2.7.3a/bin/Linux_x86_64/STAR'lib='~/biosoft/starFusion/db/GRCh38_gencode_v31_CTAT_lib_Oct012019.plug-n-play/ctat_genome_lib_build_dir/'FusionInspector --fusions SRR2016940_fusionList.txt \ ...
运行FusionInspector工具: 代码语言:javascript 代码运行次数:0 运行 AI代码解释 conda install-c bioconda fusion-inspector bin_star='~/biosoft/STAR-2.7.3a/bin/Linux_x86_64/STAR'lib='~/biosoft/starFusion/db/GRCh38_gencode_v31_CTAT_lib_Oct012019.plug-n-play/ctat_genome_lib_build_dir/'FusionIn...
I noticed a small issue when running the FusionInspector pipeline, where at the very end, it would fail with an error from create_fusion_report.py, line 7, that the igv_report module could not be found. I have already installed this module with conda and used it with the CTAT workflow...
conda install -c bioconda starseqr First make sure the dependencies are installed and generate a STAR index for your reference. RNA Index STAR --runMode genomeGenerate --genomeFastaFiles hg19.fa --genomeDir STAR_SEQR_hg19gencodeV24lift37_S1_RNA --sjdbGTFfile gencodeV24lift37.gtf --runThrea...
conda install -c bioconda trim-galore conda install -c bioconda star-fusion 可以看到目前两个软件版本是: STAR --version 2.7.10a STAR-Fusion --version STAR-Fusion version: 1.6.0 perl --version This is perl 5, version 26, subversion 2 (v5.26.2) builtforx86_64-linux-thread-multi ...