Jason Williams

wrangling-genomics/04-variant_calling: IGV output

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Following the instructions, my IGV (2.3.72 does not look exactly like the image) It's possible I haven't followed instructions thoroughly, but posting in case others can confirm or deny. [](url)

I don't think it is a good idea to import files from ENA during the workshop

wrangling-genomics/04-variant_calling: download of fastq should have a download-free option

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In general - I would like to avoid downloads, but that is a personal preference. If there is an alternative in the backup directory instructions should appear here.

Maybe an accessibility issue? Get rid of >'s in final trimmomatic loop so it can be copied/pasted

this command `scp [email protected]:~/dc_workshop/results/fastqc_untrimmed_reads/*.html ~/Desktop/fastqc_html` overwrites all files into a single invalid file. Maybe just do this `scp [email protected]:~/dc_workshop/results/fastqc_untrimmed_reads/*.html ~/Desktop`

Inconsistent with the previous lesson on loops, the variable $filename does not have braces in the example

Since we are generally copy the backup files The following command: ``` cp ~/.backup/untrimmed_fastq/*fastq.gz . ``` Could just be: ``` cp ~/.backup/untrimmed_fastq/* . ``` Since the next NexteraPE-PE.fa adapter file...

The download of the bacterial reference would be a good place to talk about checksums. Also didn't check, but is there a download-free backup for this?

I know the lesson states the following is not a valid command ``` $ bwa mem ref_genome.fasta input_file_R1.fastq input_file_R2.fastq > output.sam ``` But I would not put it in the...

Having trouble replicating the TVIEW step on the docker image and on the AWS image, anyone else. On docker I get: ```` Error opening terminal: xterm-256color. ```` On AWS (where...