文件名称：RNAseq-Analysis
文件大小：15.3MB
文件格式：ZIP
更新时间：2024-06-06 14:05:04
Shell
RNA序列 这些脚本用于处理RNAseq数据 删除旧仓库，并使用以下命令克隆新仓库： WORKING_DIR = $（pwd）; cd / srv / gsfs0 / projects / snyder / chappell / scripts; rm -rf RNAseq-分析； git clone ; chmod 777 ./RNAseq-Analysis/*; cd“ $ WORKING_DIR”
【文件预览】：
RNAseq-Analysis-master
----README.md(302B)
----RNAseq_analysis_pipeline_from_UGA.xlsx(22KB)
----4 Functional Analysis & Visualization()
--------Green Heatmap Color Key Hi-Res.pdf(156KB)
--------.Rhistory(3KB)
--------Clustering and Heatmaps.xlsx(35KB)
--------Heatmap Color Key Hi-Res.png(124KB)
--------.Rapp.history(0B)
----gunzip.sh(257B)
----1 FASTQ Trimming and QC()
--------fastqc.sh alias(1KB)
--------TrimGalore.sh alias(1016B)
----RNAseq analysis.docx(104KB)
----2014.09 Galaxy Workshop ()
--------2014.09 Galaxy Workshop - Hands-on.pdf(1.88MB)
--------2014.09 Galaxy Workshop - Intro.pdf(2.12MB)
--------2014.09 Galaxy Workshop RNA-Seq Best Practices Workflows.pdf(1.68MB)
----hESC differentiations()
--------2013 Meissner- hESC diffn RNAseq.xlsx(2.75MB)
--------2013 Meissner- hESC diffn RNAseq.pdf(2.84MB)
----RNAseq Differential Expression - Pipeline Comparison .xlsx(9KB)
----IGV tracks()
--------GRCh37v19.lnc_pro-code.transcripts.bed(5.09MB)
--------GRCh37v19.genes.bed(2.06MB)
----3 Differential Expression()
--------EBseq.multi_condition.sh(3KB)
--------DESeq2_with_examples_dont_move()
--------rsem-generate-data-matrix.sh(2KB)
--------EBseq.median_norm_of_counts.sh(547B)
--------generate_TPM_matrix.pl(2KB)
--------.Rapp.history(0B)
--------EBseq.2_condition.sh(3KB)
----2 Mapping and Quantification()
--------Prepare_Indexes()
--------STAR_RSEM-qsub_commands.xlsx(20KB)
--------STAR_RSEM_ENCODE.sh(7KB)
--------STARmanual.pdf(259KB)
--------Cufflinks.sh(1KB)
--------STAR_RSEM_ENCODE_unstranded.sh(6KB)
--------STAR_RSEM_ENCODE_stranded.sh(5KB)
----.Rhistory(1022B)
----rseqc-infer_experiment.py(379B)
----AnimalTFDB_TFs.txt(95KB)
----From Nathan()
--------STAR_RSEM_streamlined_from Nathan.sh(2KB)
--------Prep_genomes_for_STAR_and_RSEM_from_Nathan.sh(1KB)
----bam2fastq.sh(672B)
----2A Mapping QC()
--------rRNA_removal()
--------get_read_distribution.sh(784B)
--------RNAseq-mapping_QC.sh(3KB)
----Correlate with other celltypes()
--------ENCODE primary cells fastq metadata.xlsx(31KB)