Meeta Mistry

The new directory created by @upendrabhattarai is `RNA_seq_part_1`. Once everything we need is here and paths updated in the lesson we will delete: `rna-seq_2023_02` and `intro_rnaseq_hpc`

is this recommended (versus mapping-based) - need to find a benchmarking paper

add in this workshop or Peak analysis?

in troubleshooting lesson: https://hbctraining.github.io/Investigating-chromatin-biology-ChIPseq/lessons/troubleshooting_chipseq_partI.html a section on multiqc was added - I think it can be revised/polished

remove "land et al" image source and add Harvard Chan Bioinformatics Core in each image

we should specify the peak analysis workshop and add a link whenever we see this in the lessons

All tools (gene and transcript level DE) can be summarized in a table format instead of having paragraphs of text

The sequencing technologies slide deck could be updated with new rnaseq technologies from nanopore https://nanoporetech.com/rna also just check whether this info is correct

I think it would be useful to have some example scenarios of data/experimental design and ask participants to consider which workflow would be most appropriate

motif analysis upgrades

1

Do we want use MEME? It didn't run in class Also, we need to add motif enrichment analysis (rather than novel motif, followed by motif comparison)