Prophase-I-Transcription-Project/RNA-seq transcript quantification at main · Danko-Lab/Prophase-I-Transcription-Project · GitHub

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##Directory: /local/storage/projects/prophaseI/Limmaradnormalized/proseqvsrnaseq
##Date: 08/17/21

---
title: "RNAseq_analysis"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

## 1. Get counts from fastq files using Salmon https://github.com/Sethupathy-Lab/RNAseq_pipeline
wget http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M6/gencode.vM6.transcripts.fa.gz #not needed

conda install refgenie

export REFGENIE='genome_config.yaml'
/home/aka72/miniconda3/bin/refgenie init -c $REFGENIE

/home/aka72/miniconda3/bin/refgenie listr

/home/aka72/miniconda3/bin/refgenie pull mm10/salmon_sa_index

/home/aka72/miniconda3/bin/refgenie seek mm10/salmon_sa_index

##Index for salmon
/home/aka72/alias/mm10/salmon_sa_index/default/.

/home/aka72/miniconda3/bin/salmon quant -i /home/aka72/alias/mm10/salmon_sa_index/default/. -l U -p 8 -r D_R1.fastq --validateMappings -o ./DR1transcripts_quant

/home/aka72/miniconda3/bin/salmon quant -i /home/aka72/alias/mm10/salmon_sa_index/default/. -l U -p 8 -r D_R2.fastq --validateMappings -o ./DR2transcripts_quant

/home/aka72/miniconda3/bin/salmon quant -i /home/aka72/alias/mm10/salmon_sa_index/default/. -l U -p 8 -r D_R3.fastq --validateMappings -o ./DR3transcripts_quant

/home/aka72/miniconda3/bin/salmon quant -i /home/aka72/alias/mm10/salmon_sa_index/default/. -l U -p 8 -r LZ_R1.fastq --validateMappings -o ./LZR1transcripts_quant

/home/aka72/miniconda3/bin/salmon quant -i /home/aka72/alias/mm10/salmon_sa_index/default/. -l U -p 8 -r LZ_R2.fastq --validateMappings -o ./LZR2transcripts_quant

/home/aka72/miniconda3/bin/salmon quant -i /home/aka72/alias/mm10/salmon_sa_index/default/. -l U -p 8 -r LZ_R3.fastq --validateMappings -o ./LZR3transcripts_quant

/home/aka72/miniconda3/bin/salmon quant -i /home/aka72/alias/mm10/salmon_sa_index/default/. -l U -p 8 -r P_R1.fastq --validateMappings -o ./PR1transcripts_quant

/home/aka72/miniconda3/bin/salmon quant -i /home/aka72/alias/mm10/salmon_sa_index/default/. -l U -p 8 -r P_R2.fastq --validateMappings -o ./PR2transcripts_quant

/home/aka72/miniconda3/bin/salmon quant -i /home/aka72/alias/mm10/salmon_sa_index/default/. -l U -p 8 -r P_R3.fastq --validateMappings -o ./PR3transcripts_quant