From 3f6dd3ebbc5c8e8522a4f851db85df707eb5c9a8 Mon Sep 17 00:00:00 2001 From: Steven Roberts Date: Fri, 2 Jun 2023 10:35:00 -0700 Subject: [PATCH 1/3] SR --- code/05-kallisto.Rmd | 21 ++--- code/05-kallisto.html | 86 +++++-------------- .../rpubs.com/rpubs/Document.dcf | 11 +++ 3 files changed, 36 insertions(+), 82 deletions(-) create mode 100644 code/rsconnect/documents/05-kallisto.Rmd/rpubs.com/rpubs/Document.dcf diff --git a/code/05-kallisto.Rmd b/code/05-kallisto.Rmd index de35ac0..2ff37ef 100644 --- a/code/05-kallisto.Rmd +++ b/code/05-kallisto.Rmd @@ -35,7 +35,8 @@ knitr::opts_chunk$set( ``` -**Data**\ +# **Data** + Existing RNA-Seq data was retrieved from the following complete RNASeq data available in the [NCBI database](https://www.ncbi.nlm.nih.gov/):\ - SRR19782039 [Exposure to Valsartan & Carbamazepine](https://www.ncbi.nlm.nih.gov/sra/SRX15826291%5Baccn%5D)\ - SRR16771870 [Exposure to a synthetic hormone 17 a-Ethinylestradiol (EE2)](https://www.ncbi.nlm.nih.gov/sra/SRX12971792%5Baccn%5D)\ @@ -50,18 +51,13 @@ cp /home/shared/8TB_HDD_01/sr320/ncbi/ncbi_dataset/data/GCA_900618805.1/cds_from ``` - - -### Pulling my reference genome from prefab code provided by NCBI -curled genome and copied just cds file - ```{r, engine='bash', eval=TRUE} head ../data/cds_from_genomic.fna ``` +# Index Gene Set - -# Create the index file to align my short read files to the genes from the MGAL_10 +Create the index file to align my short read files to the genes from the MGAL_10 ```{r, engine='bash'} /home/shared/kallisto/kallisto \ index \ @@ -70,12 +66,7 @@ index \ ``` - - -# Where is data - - -#Runnning Kallisto +# Runnning Kallisto ```{r, engine='bash', eval=TRUE} /home/shared/kallisto/kallisto quant @@ -89,8 +80,6 @@ ls /home/shared/8TB_HDD_02/cnmntgna/GitHub/chris-musselcon/output/ncbi/ #mkdir ../output #mkdir ../output/kallisto_01 -#OLD CODE - find /home/shared/8TB_HDD_02/cnmntgna/GitHub/chris-musselcon/output/ncbi/*_1.fastq 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