| STAR_INDEX="/home/mRNAseq/ref/gencode/human/GRCh37.19/idx/" | |
| INPUT_DIR="00_raw_fastq" | |
| OUTPUT_DIR="01_alignment" | |
| GTF="/home/mRNAseq/ref/gencode/human/GRCh37.19/gtf/gencode.v19.annotation.gtf" | |
| RSEM_INDEX="/home/mRNAseq/ref/gencode/human/GRCh37.19/idx/GRCh37.p13.genome" | |
| mkdir -p $OUTPUT_DIR | |
| cat samples.list | parallel --jobs 1 "mkdir -p $OUTPUT_DIR/{}" | |
| cat samples.list | parallel --jobs 1 "rsem-calculate-expression --estimate-rspd --paired-end -p 25 --star --star-gzipped-read-file --keep-intermediate-files $INPUT_DIR/{}_1.fastq.gz $INPUT_DIR/{}_2.fastq.gz /home/mRNAseq/ref/gencode/human/GRCh37.19/idx/GRCh37.p13.genome $OUTPUT_DIR/{}/" |
| ls *R1* | sed 's/_R1.fastq.gz//' | parallel "echo {}_R1.fastq.gz {}_R2.fastq.gz" |
| Sys.setlocale(category="LC_ALL", locale = "korean") | |
| read.csv(fileEncoding = "UTF-8") |
| #!/usr/bin/env python | |
| from __future__ import division | |
| __author__ = "Jai Ram Rideout" | |
| __copyright__ = "Copyright 2012, The QIIME project" | |
| __credits__ = ["Jai Ram Rideout"] | |
| __license__ = "GPL" | |
| __version__ = "1.9.1" | |
| __maintainer__ = "Jai Ram Rideout" | |
| __email__ = "[email protected]" |
| # HGEN 473 - Genomics | |
| # Spring 2017 | |
| # Tuesday, May 9 & Thursday, May 11 | |
| # | |
| # RNA-seq analysis with R/Bioconductor | |
| # | |
| # John Blischak | |
| # Introduction ------------------------------------------------------- |
The IPython Notebook has two different keyboard input modes. Edit mode allows you to type code/text into a cell and is indicated by a green cell border. Command mode binds the keyboard to notebook level actions and is indicated by a grey cell border.