From ed9f0fd16200fcdfd86d01618bcf407fa11288b4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Camilo=20Garc=C3=ADa?= Date: Sun, 17 Apr 2022 21:02:30 -0500 Subject: [PATCH] render previous seven commits including cache --- .quarto/crossref/index.qmd/index.html.json | 2 +- .../references.qmd/references.html.json | 2 +- demo-genome-searching_cache/html/__packages | 7 ---- ...ing_91bdbc4dd42bab566973aec10221dbcd.RData | Bin 0 -> 335 bytes ...ssing_91bdbc4dd42bab566973aec10221dbcd.rdb | 0 ...ssing_91bdbc4dd42bab566973aec10221dbcd.rdx | Bin 0 -> 125 bytes ...ing_99207958b71348f644a376668f84e5aa.RData | Bin 0 -> 287 bytes ...ading_99207958b71348f644a376668f84e5aa.rdb | 0 ...ading_99207958b71348f644a376668f84e5aa.rdx | Bin 0 -> 125 bytes demo-phylogenetics_cache/html/__packages | 5 +++ ...k-1_5f67f100fe84738a6334ee503853aa01.RData | Bin 0 -> 174 bytes ...unk-1_5f67f100fe84738a6334ee503853aa01.rdb | 0 ...unk-1_5f67f100fe84738a6334ee503853aa01.rdx | Bin 0 -> 125 bytes 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Table of contents

    -
  • Challenge
    • -
  • Download the reads
    • +
  • Download the reads
  • Assess read qualities
  • Exploring assemblers
      @@ -334,11 +333,20 @@

      15  -
      -

      Challenge

      +
      +
      +
      + +
      +
      +Challenge +
      +
      +

      Your professor has sequenced a bacterial isolate using PacBio and Nanopore sequencing methods and has got the FASTQ files from both technologies. Now he needs to know the quality and quantity of these data before start any other analysis and ask you to assess the data. He needs to know how many sequences there are, how many base pairs (in GB) are there and the N50. He is also interested in see a visualization of the i) number of bases vs. sequence lengths (log transformed) and ii) the read length vs. read quality vs. read number.

      He ask you to document every step and to conclude what data should be used.

      -
      + +

      Download the reads

      wget
      diff --git a/docs/demo-genome-searching.html b/docs/demo-genome-searching.html index b3b8115..41c7934 100644 --- a/docs/demo-genome-searching.html +++ b/docs/demo-genome-searching.html @@ -272,17 +272,12 @@

      @@ -307,8 +302,19 @@

      -

      Challenge

      +
      +
      +
      + +
      +
      +Challenge +
      +
      +

      Your profesor is interested on knowing how many complete genomes of Bacillus subtilis are there in the NCBI databases. He ask you later to count the number of features (genes, CDS, ncRNA, rRNA, etc.) in the genome of Bacillus subtilis NCIB 3610 (GCF_002055965.1). And tell you to document each of the steps and how did you end up with the answer. Saving the file with your initials (e.g., CG-activity01.{md,txt,docx})

      +
      +

      Downloading a genome

      ncbi-genome-download

      Downloading from NCBI

      @@ -335,7 +341,7 @@

      Importing the files into R

      -
      +
      library(tidyverse)
 library(fs)
 
@@ -375,7 +381,7 @@

      Data processing

      -
      +
      all_features_grouped <- all_features %>% 
   rename(feature = `# feature`) %>% 
   select(assembly, feature) %>% 
@@ -390,7 +396,7 @@ 
      
 
      create a new dataset that will group by features per accession. get read of the weird name of the column. Select these two columns. Group by these two columns to perform. count the numbers of rows based on the applied group. generate a wide dataset sending row names as columns. Arrange descending by the number of CDSs.
      
 
 
-