STAR下载地址
2018-08-28 本文已影响20人
11的雾
STAR下载地址
https://github.com/alexdobin/STAR
下载安装：
tar -xzf 2.5.3a.tar.gz
cd STAR-2.5.3a
make STAR
建立索引：
/cygene/work/STAR-2.5.3a/source/STAR \
--runThreadN 20 \
--runMode genomeGenerate \
--genomeDir ./ \
--genomeFastaFiles /home/dushiyi/database/refdata-cellranger-GRCh38-1.2.0/fasta/genome.fa \
--sjdbGTFfile /home/dushiyi/database/refdata-cellranger-GRCh38-1.2.0/genes/genes.gtf
20个线程，大约耗时35分钟。消耗内存30G，
$ sh work.sh
Aug 28 09:16:14 ..... started STAR run
Aug 28 09:16:14 ... starting to generate Genome files
Aug 28 09:17:10 ... starting to sort Suffix Array. This may take a long time...
Aug 28 09:17:24 ... sorting Suffix Array chunks and saving them to disk...
Aug 28 09:58:43 ... loading chunks from disk, packing SA...
Aug 28 10:01:53 ... finished generating suffix array
Aug 28 10:01:53 ... generating Suffix Array index
Aug 28 10:04:37 ... completed Suffix Array index
Aug 28 10:04:37 ..... processing annotations GTF
Aug 28 10:04:50 ..... inserting junctions into the genome indices
Aug 28 10:07:26 ... writing Genome to disk ...
Aug 28 10:07:28 ... writing Suffix Array to disk ...
Aug 28 10:09:05 ... writing SAindex to disk
Aug 28 10:09:22 ..... finished successfully
比对：
/cygene/work/STAR-2.5.3a/source/STAR \
--runThreadN 20 \
--genomeDir /cygene/work/02.dropEst/star \
--readFilesCommand zcat \
--outSAMtype BAM Unsorted \
--readFilesIn /cygene/work/02.dropEst/01_dropTag/sample1.fastq.gz.tagged.fastq.gz
20线程，耗时 内存
