more misc changes

_posts/0000-10-01-Installation.md

@@ -14,7 +14,7 @@ date: 0000-10-01
 First, make sure your [environment](https://rnabio.org/module-00-setup/0000/07/01/Environment/) is set up correctly.
 
 ***
-Tools needed for this analysis are: samtools, bam-readcount, HISAT2, stringtie, gffcompare, htseq-count, flexbar, R, ballgown, fastqc and picard-tools. In the following installation example, the installs are local and will work whether you have root (i.e. admin) access or not. However, if root is available some binaries can/will be copied to system-wide locations (e.g., ~/bin/).
+Tools needed for this analysis are: samtools, bam-readcount, HISAT2, stringtie, gffcompare, htseq-count, gtf_to_fasta (TopHat), kallisto, FastQC, Fastp, MultiQC, Picard, flexbar, Regtools, RSeqQC, bedops, gtfToGenePred, genePredToBed, how_are_we_stranded_here, CellRanger, R, BioConductor, ballgown, and other R packages. In the following installation example, the installs are local and will work whether you have root (i.e. admin) access or not. However, if root is available some binaries can/will be copied to system-wide locations (e.g., ~/bin/).
 
 Set up tool installation location:
 

_posts/0002-07-01-Team_Assignment_Alignment.md

@@ -46,9 +46,9 @@ In this assignment, we will be using subsets of the GSE136366 dataset (Roczniak-
 
 As mentioned previously, we have subsetted the 6 RNA-seq samples into 5 different chromosome regions. Each team can download their corresponding dataset using the following commands.
 ```bash
-mkdir -p $RNA_HOME/team_exercise/data
-cd $RNA_HOME/team_exercise/data
-
+cd $RNA_HOME/
+mkdir -p team_exercise/untrimmed
+cd team_exercise/untrimmed
 
 ### TEAM A
 wget -c http://genomedata.org/seq-tec-workshop/read_data/rna_alignment-de_exercise/dataset_A/dataset.tar.gz