# 参考: https://mp.weixin.qq.com/s/kG2uI3me8Xo69mClThRutA salmon index -t Bos_taurus.ARS-UCD1.2.cdna.all.fa -i Bos_taurus.ARS-UCD1.2.cdna.salmon.index 得到的salmon的index是一个文件夹,内容如下: ls -lh Bos_taurus.ARS-UCD1.2.cdna.salmon.index/|cut -d" " -f 5- 4.4K May 9 ...
然后去:http://asia.ensembl.org/Bos_taurus/Info/Index可以看到参考基因组和参考转录组的下载地址: 点击进去就可以看到最新版地址了,因为要演示salmon流程,仅仅是需要参考转录组序列的fasta文件即可,代码如下: wget http://ftp.ensembl.org/pub/release-104/fasta/bos_taurus/cdna/Bos_taurus.ARS-UCD1.2.cdna.all...
/bin/rm -rf GRCh38.salmon_sa_index /usr/bin/time -o Salmon_human_genome.log -v salmon index -t GRCh38_trans_genome.fa -d GRCh38.decoys.txt -i GRCh38.salmon_sa_index -p 2 du -s GRCh38_trans_genome.fa | awk 'BEGIN{OFS="\t"}{print "Genome_size: "$1/10^6}' >>Salmon_h...
salmon_sa_index_tmp -p 2 du -s GRCh38_trans_genome.fa | awk 'BEGIN{OFS="\t"}{print "Genome_size: "$1/10^6}' >>Salmon_human_genome_${i}.log du -s GRCh38.transcript_tmp.fa | awk 'BEGIN{OFS="\t"}{print "Transcript_size: "$1/10^6}' >>Salmon_human_genome_${i}.log...
build index 代码语言:javascript 代码运行次数:0 运行 AI代码解释 kallisto index -i kallisto_index/Mus_musculus.GRCm38 Mus_musculus.GRCm38.cdna.all.fa salmon index -i salmon_index/Mus_musculus.GRCm38 -t Mus_musculus.GRCm38.cdna.all.fa -p 20 生成批量运行的脚本 准备文件:samples.path.tsv(原始...
index: Build a de novo splicing annotation index of events custom to your data Google search:get PSI value for one exon【PSI值没那么好算,最好把它底层的逻辑搞懂】 PSI,非常简单明确,就是inclusion reads / (inclusion reads + exclusion reads) ...
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cDNA-only index : salmon_index -https://combine-lab.github.io/salmon/getting_started/. This method will result in the smallest index and require the least resources to build, but will be the most prone to possible spurious alignments. ...
git clone https://github.com/your-username/simple-node-http-server.gitcdsimple-node-http-server Usage Run the server using Node.js: node index.js The server will start onhttp://localhost:3000. API GET / Returns a simple welcome message. ...
specific version of salmon that was used to build the index. TheindexVersionfield is already a version identifier that is incremented when the index changes in a binary-incompatible way. However, the new field will allow one to know the exact salmon version that was used to build the index....