Install Java

Use sdkman

curl -s "https://get.sdkman.io" | bash
source "$HOME/.sdkman/bin/sdkman-init.sh"
sdk version
If it goes well, you can see sdkman 5.15.0
sdk install java

go to Installation of Java from nextflow docs or sdkman

Next Generation Sequencing file Formats

great documentation by Pierre Lindenbaum

Secondary alignment

A secondary alignment refers to a read that produces multiple alignmentsin the genome. One of these alignments will be typically referred to as the“primary” alignment.

Supplementary alignment

A supplementary alignment (also known as a chimeric alignment) is an align-ment where the read partially matches different regions of the genome with-out overlapping the same alignment.

Docker

docker run -v ${PWD}:/docker/ quay.io/biocontainers/fastqc:0.11.9--0 fastqc /docker/data/ggal/gut-1.fq -o /docker/fastqc-out -v ${PWD} host machine current dir :/docker/ docker container

Git

git remote add origin https://github.com//your-project.git

git push -u origin main

fastqc

well explained

https://rtsf.natsci.msu.edu/sites/_rtsf/assets/File/FastQC_TutorialAndFAQ_080717.pdf

https://hbctraining.github.io/Intro-to-rnaseq-hpc-salmon/lessons/qc_fastqc_assessment.html

https://www.sc-best-practices.org/introduction/raw_data_processing.html

nextflow

https://carpentries-incubator.github.io/workflows-nextflow/01-getting-started-with-nextflow/index.html

singularity

singularity exec --cleanenv -H $PWD  --bind $PWD:/$PWD /mnt/beegfs/kimj32/singularity/tidyverse_1.0.0.sif Rscript $PWD/star_to_mat.R $PWD/analysis/star/

Be aware that singularity can't follow symlinks.

singularity run --bind analysis/sing:/data/ ~/beegfs/singularity/multiqc.sif multiqc /data/

Your home directory (or current directory, on older versions) on the host machine is mounted in and used as the working directory inside the container. You can use the --pwd flag to override this.

See https://stackoverflow.com/questions/65642199/difference-between-working-directory-of-docker-and-singularity

housekeeping gene list

housekeepers.txt: list of 98 housekeeping genes compiled in Tirosh et al., 2016, to be used in data preprocessing, to remove sources of unwanted variation See https://github.com/Michorlab/tnbc_scrnaseq

Google tricks

Add [r] to search R programming related pages. i.e. "rotate x axis label [python]
Use quotations " " to searech for the exact phrase.
Add a tilde ~ in front of a word to find synonyms.
Exclude terms with a minux - symbol.
Search specific sites with site: e.g. "heatmap site:https://support.binconductor.org"
Define a filetype by : heatmap filetype:pdf. It will only give you PDF files in the results. -from Dr. Ming Tang (https://www.youtube.com/watch?v=qg3FP2CCeRw)

List of illumina adapter sequences

See https://knowledge.illumina.com/library-preparation/general-library-preparation/library-preparation-general-reference_material-list/000001314

Specific problems for illumina libraries

https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial.html

illumina index sequence

https://github.com/faircloth-lab/illumiprocessor/blob/main/docs/usage.rst

font

https://www.koddi.or.kr/ud/sub1_2

illumina regarding lanes

Standard workflow allows for one library pool to be loaded in all lanes of the flow cell. On the other hand, the XP workflow enables the sequencing of different library pools in each lane of the Novaseq flow cells.