Difference between revisions of "HLab:Steps"
From CCGB
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== HiSeq 2000 == | == HiSeq 2000 == | ||
# Make sure sample sheet does not include quotes. | # 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 | # 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. | #* output-dir should be under fastq directory, year, run folder, then fastq. | ||
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# Put symlinks in production folder pointing to fastq files | # Put symlinks in production folder pointing to fastq files | ||
# Copy data from illumina-9 to rawseq folder | # Copy data from illumina-9 to rawseq folder | ||
| + | # Copy reports and status files to runReports folder, make link in run table | ||
== NextSeq 500 == | == NextSeq 500 == | ||
# Copy data from learfan back to rawseq directory. | # Copy data from learfan back to rawseq directory. | ||
# Copy sample sheet to top directory of run folder, name must be SampleSheet.csv | # 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 | # 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) | #* needs min 16G RAM per core (3x16=48G out of 60G) | ||
# Make symlinks in fastq folder to rawseq Data/Intensities/BaseCalls | # Make symlinks in fastq folder to rawseq Data/Intensities/BaseCalls | ||
# Put symlinks in production folder pointing to fastq files | # 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== | ==Trouble shooting== | ||
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#*:where target = win, mac, or unix | #*:where target = win, mac, or unix | ||
#*:Example: /afs/bx.psu.edu/home/cathy/bin/line-ends unix run26_SampleSheet.csv > run26_SampleSheet_endunix.csv | #*:Example: /afs/bx.psu.edu/home/cathy/bin/line-ends unix run26_SampleSheet.csv > run26_SampleSheet_endunix.csv | ||
| + | |||
| + | Return to [[HLab:Main]] | ||
Latest revision as of 14:56, 19 December 2014
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
- Usage: /afs/bx.psu.edu/home/cathy/bin/line-ends <target> <filename> > output
- where target = win, mac, or unix
- Example: /afs/bx.psu.edu/home/cathy/bin/line-ends unix run26_SampleSheet.csv > run26_SampleSheet_endunix.csv
- ~cathy/bin/line-ends
Return to HLab:Main
