This document is the beginning of a training document to describe the process from data curation from the novaseq, bcl2fastq conversion, indexing for metadata, archival to tape, validation, labeling, retrieval.<\/p>\n
Data from a novaseq run is controlled via the novaseq machine – novaseqdata has a samba share which the machine can see from the front end program. This is selected and created at the start of a run giving the run it’s name and directory. Data written here is as sbsuser and that also translates into sbsuser on novaseqdata<\/p>\n
After the run is complete the data is run through a run through a program to extract fastq data<\/p>\n
bcl2fastq<\/strong><\/p>\n ssh into novaseqdata as sbsuser<\/p>\n run the bcl2fastq command\u00a0 – run from within the \/mnt\/novaseqdata\/training\/180525_A00471_0028_AHCKH2DMXX<\/p>\n Note:<\/strong> ignore \\ in the following listings – type it all in on one line.<\/p>\n The process can take a couple of hours from start to finish depending on the run type – S2 or S4<\/p>\n CellRanger<\/strong><\/p>\n Note:<\/strong> ignore \\ in the following listings – type it all in on one line.<\/p>\n The process can take an hour or so to run – creates HF7JJDRXX as a subdirectory\u00a0 which has the fastq files written within it<\/p>\n index the directory data with tree<\/strong><\/p>\n From within the \/mnt\/novaseqdata\/training\/180525_A00471_0028_AHCKH2DMXX run directory issue this command<\/p>\n tape backup and restore<\/strong> * see later entry for tape manipulation in the library<\/p>\n From within the \/mnt\/novaseqdata\/training directory issue this command<\/p>\n To restore the data from tape: –<\/p>\n rsync from novaseqdata to rocket<\/strong><\/p>\n Trailing slashes are important – if there is no upstream directory 180525_A00471_0028_AHCKHSDMXX rsync will create it and write data\u00a0 into it accordingly. (NB can’t have more than one \/ separation upstream I discovered)<\/p>\n Once done it needs to be chmod’d recursively to 775 for other people from the group to access it: –<\/p>\n This document is the beginning of a training document to describe the process from data curation from the novaseq, bcl2fastq conversion, indexing for metadata, archival to tape, validation, labeling, retrieval. Data from a novaseq run is controlled via the novaseq machine – novaseqdata has a samba share which the machine can see from the front […]<\/a><\/p>\n","protected":false},"author":4848,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-1431","post","type-post","status-publish","format-standard","hentry","category-uncategorized","category-1-id","post-seq-1","post-parity-odd","meta-position-corners","fix"],"_links":{"self":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/1431","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/users\/4848"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=1431"}],"version-history":[{"count":15,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/1431\/revisions"}],"predecessor-version":[{"id":1469,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/1431\/revisions\/1469"}],"wp:attachment":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1431"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1431"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1431"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}cd \/mnt\/novaseqdata\/training\/180525_A00471_0028_AHCKH2DMXX<\/pre>\n
nohup \/usr\/local\/bin\/bcl2fastq -R \\\r\n\/mnt\/novaseqdata\/training\/180525_A00471_0028_AHCKH2DMXX -o \\\r\n\/mnt\/novaseqdata\/training\/180525_A00471_0028_AHCKH2DMXX --sample-sheet \\\r\n\/mnt\/novaseqdata\/training\/180525_A00471_0028_AHCKH2DMXX\/SampleSheet.csv<\/pre>\n
cd \/mnt\/novaseqdata\/training\/190823_A00471_0062_BHF7JJDRXX\/<\/pre>\n
\/opt\/cellranger-3.0.2\/cellranger mkfastq --run=\/mnt\/novaseqdata\/training\/ \\\r\n190823_A00471_0062_BHF7JJDRXX\/ \\\r\n--samplesheet=\/mnt\/novaseqdata\/training\/ \\\r\n190823_A00471_0062_BHF7JJDRXX\/sample_sheet_dan_williamson.csv\r\n\r\n<\/pre>\n
tree -a -T '180525_A00471_0028_AHCKH2DMXX' -H \\\r\n\/mnt\/novaseqdata\/training\/180525_A00471_0028_AHCKH2DMXX -o index.html \\\r\n\/mnt\/novaseqdata\/training\/180525_A00471_0028_AHCKH2DMXX<\/pre>\n
cd \/mnt\/novaseqdata\/training\/\r\ntar -cMvf \/dev\/st0 180525_A00471_0028_AHCKH2DMXX\/*<\/pre>\n
cd \/tmp\r\ntar -xMvf \/dev\/st0 180525_A00471_0028_AHCKH2DMXX\/*\r\nor\r\ntar -xMvf \/dev\/st0<\/pre>\n
rsync -av \\\r\n\/mnt\/novaseqdata\/training\/180525_A00471_0028_AHCKH2DMXX \r\nnbh23@rocket.hpc.ncl.ac.uk:\/nobackup\/proj\/scbsu\/<\/pre>\n
chmod -R 775 \/nobackup\/proj\/scbsu\/180525_A00471_0028_AHCKH2DMXX\/<\/pre>\n","protected":false},"excerpt":{"rendered":"