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==Tools== * RnBeads resources: http://rnbeads.mpi-inf.mpg.de/methylomes.php * Note on how to set up passwordless login (linux): http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2015/NOTES/2015-5-7 * Note on how to download fastq file from BaseSpace account without using Web-based GUI: http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2015/NOTES/2015-3-25 * Convert oligos grams to pmol: http://www.promega.com/a/apps/biomath/index.html?calc=ugmlpmolul * Quickly check DMRs methylation in WGBS data: http://bioinfo2.ugr.es/NGSmethDB/NGSmethDBviewer.php?assembly=hg19 * Venn Diagram plotter, http://bioinformatics.psb.ugent.be/webtools/Venn/ * "Sushi.R : flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures" * Dual booting guide for Linux-Os X: http://www.rodsbooks.com/ubuntu-efi/ * WGET command (useful for downloading from other lab's servers via web server or FTP): wget --user=USERNAME --password='PASSWORD' -c -nH --cut-dirs=2 -U mozilla -r -np --convert-links --reject="index.html*" -e robots=off http://enhancer.sdsc.edu/bli/brandon/Data/ * Demultiplexing Mi-Seq runs on genome-miner: Make a new directory & go into this directory first. Then type the following commands (change MiSeq output folder and date!): ln -s /media/LTS_60T/SeqStore2016/MiSeqAnalysis/160419_M00159_0174_000000000-ANULK/Data Data cp /media/LTS_60T/SeqStore2016/MiSeqAnalysis/160419_M00159_0174_000000000-ANULK/SampleSheet.csv . cp /media/LTS_60T/SeqStore2016/MiSeqAnalysis/160419_M00159_0174_000000000-ANULK/RunInfo.xml . bcl2fastq -o 160419_MiSeq --sample-sheet SampleSheet.csv --barcode-mismatches 0 * Derek's instructions for MiSeq Notes from August 24th 2016: http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2016/NOTES/2016-8-24
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