Merge branch 'main' of https://github.com/course-fish546-2023/chris-m…

…usselcon
course-fish546-2023 · Jun 2, 2023 · 3e1ca51 · 3e1ca51
2 parents dfc157d + 10862c3
commit 3e1ca51
Show file tree

Hide file tree

Showing 5 changed files with 2,608 additions and 82 deletions.
diff --git 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 \
 | xargs basename -s _1.fastq  | xargs -I{} /home/shared/kallisto/kallisto \
 quant -i ../data/MGAL_cds.index \

diff --git a/code/05-kallisto.html b/code/05-kallisto.html
diff --git a/code/07-blastingCDS.qmd b/code/07-blastingCDS.qmd
@@ -232,7 +232,12 @@ library(kableExtra)
 library(knitr)
 library(dplyr)
 library(readr)
+#new table process
+full <-left_join(cdsDEG, uni, by = c("Column 2" = "Entry"))
+write.table(full, file = "/home/shared/8TB_HDD_02/cnmntgna/GitHub/chris-musselcon/data/annoblast.tab", sep = "\t", row.names = FALSE)
+```
 
+```{r}
 # Generate table
 kbl(
   head(

diff --git a/code/rsconnect/documents/05-kallisto.Rmd/rpubs.com/rpubs/Document.dcf b/code/rsconnect/documents/05-kallisto.Rmd/rpubs.com/rpubs/Document.dcf
@@ -0,0 +1,11 @@
+name: Document
+title:
+username:
+account: rpubs
+server: rpubs.com
+hostUrl: rpubs.com
+appId: https://api.rpubs.com/api/v1/document/1033647/813bc1a525b94585a7a2ddc1eb48233e
+bundleId: https://api.rpubs.com/api/v1/document/1033647/813bc1a525b94585a7a2ddc1eb48233e
+url: http://rpubs.com/publish/claim/1033647/6e7075d73dc34714a6321f17180b1d99
+when: 1682452314.04458
+lastSyncTime: 1682452314.04459