RNASeq

RNASeq FIles

Building RNASeq pipelines, with multiple functionality. This repository includes pipelines for paired-end and single-end, mapping with STAR, HISAT2, or unmapped quantifiers like Salmon.

Name		Name	Last commit message	Last commit date
CSVs		CSVs
New_CSVs		New_CSVs
HISAT2_aligned_report.html		HISAT2_aligned_report.html
PRODMAT_samples.txt		PRODMAT_samples.txt
README.md		README.md
Untitled.md		Untitled.md
compare_sheets.py		compare_sheets.py
counts_merge.py		counts_merge.py
execute.sh		execute.sh
flagstat.sh		flagstat.sh
github_setup.sh		github_setup.sh
helpful_code.txt		helpful_code.txt
kallisto.sh		kallisto.sh
multiqc.sh		multiqc.sh
multiqc_report.html		multiqc_report.html
qualimap.sh		qualimap.sh
rnaseq.yml		rnaseq.yml
rnaseq_pipeline.ipynb		rnaseq_pipeline.ipynb
run-pipe-PE-HISAT2-hg38.sh		run-pipe-PE-HISAT2-hg38.sh
run-pipe-PE-STAR-hg38.sh		run-pipe-PE-STAR-hg38.sh
run-pipe-SE-STAR-hg38.sh		run-pipe-SE-STAR-hg38.sh
test_R1_001.fastq.gz		test_R1_001.fastq.gz
test_R2_001.fastq.gz		test_R2_001.fastq.gz
test_RSEM.sh		test_RSEM.sh
tpm_merge.py		tpm_merge.py

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