View source for HLab:Steps

== HiSeq 2000 ==
# Make sure sample sheet does not include quotes.
#* requires index sequence to only be six bases
# configureBclToFastq.pl --input-dir <BaseCalls_dir> --output-dir <Unaligned> --sample-sheet <BaseCalls_dir>/SampleSheet.csv --no-eamss --mismatches 1 --fastq-cluster-count 0
#* output-dir should be under fastq directory, year, run folder, then fastq.
# cd output-dir
# On mal: (screen or) nohup make -j 4
# concat read1, read2 fastq files
# Put symlinks in production folder pointing to fastq files
# Copy data from illumina-9 to rawseq folder
# Copy reports and status files to runReports folder, make link in run table

== NextSeq 500 ==
# Copy data from learfan back to rawseq directory.
# Copy sample sheet to top directory of run folder, name must be SampleSheet.csv
#* requires all 7 bases of index in sample sheet
# On mal: (screen or) nohup '''bcl2fastq2''' --runfolder-dir ~/hlab/reorg/rawseq/<year>/<run folder> -p 3 -d 2 --barcode-mismatches 1
#* needs min 16G RAM per core (3x16=48G out of 60G)
# Make symlinks in fastq folder to rawseq Data/Intensities/BaseCalls
# Put symlinks in production folder pointing to fastq files

== MiSeq ==
# rsync rawdata back to bx from makova-miseq-cache.
# Convert to fastq if necessary (similar to HiSeq)

== HiSeq at Huck ==
# Get fastq files and Fastqc reports from ftp site (lab user name and password required).

==Trouble shooting==
# Things to make sure before you begin
# Make sure the file has unix line endings. If it was created using Excel on a Mac, it will have MacOSX line endings. Run Cathy’s line-ends program to change the line endings.
#*:~cathy/bin/line-ends<br />
#*:Usage:  /afs/bx.psu.edu/home/cathy/bin/line-ends <target> <filename> > output <br />
#*:where target = win, mac, or unix
#*:Example: /afs/bx.psu.edu/home/cathy/bin/line-ends unix run26_SampleSheet.csv > run26_SampleSheet_endunix.csv