Difference between revisions of "HLab:Steps"

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== Bcl – qseq - fastq ==
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== HiSeq 2000 ==
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===1. Get run folder name===
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# Make sure sample sheet does not include quotes.
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from Cheryl. (RUN_NAME)
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#* requires index sequence to only be six bases
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===2. Create RUN_NAME directory===
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# configureBclToFastq.pl --input-dir <BaseCalls_dir> --output-dir <Unaligned> --sample-sheet <BaseCalls_dir>/SampleSheet.csv --no-eamss --mismatches 1 --fastq-cluster-count 0
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under /afs/bx.psu.edu/depot/data/hardison_lab/illumina/bcl_to_fastq/job_output (example: mkdir 120111_SN407_0185_BD0F1EABXX )
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#* output-dir should be under fastq directory, year, run folder, then fastq.
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===3. Make a config file (CONFIG_FILE)===
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# cd output-dir
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In /afs/bx.psu.edu/depot/data/hardison_lab/illumina/bcl_to_fastq/
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# On mal: (screen or) nohup make -j 4
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Copy the previous run’s config file and change the info in it to reflect the updated information. Basically, wherever you spot the run name of some old run in this file, change it to the current RUN_NAME. Give your own email address.
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# concat read1, read2 fastq files
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===4. Submit jobs===
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# Put symlinks in production folder pointing to fastq files
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In the same directory, i.e.  /afs/bx.psu.edu/depot/data/hardison_lab/illumina/bcl_to_fastq/ run the following command:
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# Copy data from illumina-9 to rawseq folder
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# Copy reports and status files to runReports folder, make link in run table
  
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submit-jobs CONFIG_FILE
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== NextSeq 500 ==
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# Copy data from learfan back to rawseq directory.
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# Copy sample sheet to top directory of run folder, name must be SampleSheet.csv
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#* requires all 7 bases of index in sample sheet
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# On mal: (screen or) nohup '''bcl2fastq2''' --runfolder-dir ~/hlab/reorg/rawseq/<year>/<run folder> -p 3 -d 2 --barcode-mismatches 1
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#* needs min 16G RAM per core (3x16=48G out of 60G)
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# Make symlinks in fastq folder to rawseq Data/Intensities/BaseCalls
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# Put symlinks in production folder pointing to fastq files
  
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This submits jobs to the cluster (persephone). Use qstat to check on progress.  It will email at the start and end of each job.  The error and output files are written to the directory you created under job_output.  If a job errors out use qdel JOBID to delete it.  (or qdel –u username to delete all jobs)
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== MiSeq ==
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The output qseq and fastq files will be in the location specified in the CONFIG_FILE.  During the conversion to fastq the reads are filtered based on the pass filter field of the qseq file. 
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# rsync rawdata back to bx from makova-miseq-cache.
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# Convert to fastq if necessary (similar to HiSeq)
  
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Run 32 finished in about 2 hours using less than 4G of RAM.
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== HiSeq at Huck ==
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==Demultiplexing==
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# Get fastq files and Fastqc reports from ftp site (lab user name and password required).
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* Even if none of the lanes are multiplexed these steps and program will rename the fastq files (by creating symlinks).  If it is a mix it will do each lane as appropriate.  The index column in the SampleSheet should be empty for these lanes.
 
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* To demultiplex some specific lanes or all lanes, create a SampleSheet.csv in the /fastq directory of that run (FASTQ_DIRECTORY in config file). It has to have as many lines as the final number of demultiplexed files desired, with one line specifying info for each file. This is a CSV version of excel file Cheryl sends.  (As specified in CASAVA 1.7 users guide - /usr/local/CASAVA-1.7.0/share/CASAVA-1.7.0/docs/cassava/CASAVA1.7_User_Guide_15011196_A.pdf).
 
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* 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.
 
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*:::~cathy/bin/line-ends<br />
 
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*:::Usage:  /afs/bx.psu.edu/home/cathy/bin/line-ends <target> <filename> > output <br />
 
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*:::where target = win, mac, or unix
 
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*:::Example: /afs/bx.psu.edu/home/cathy/bin/line-ends unix run26_SampleSheet.csv > run26_SampleSheet_endunix.csv
 
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* The “unknown” files contains fastq reads that were not assigned to any specific index because the index sequence had mismatches.
 
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* The file RUN_NAME/fastq/info.txt has the original fastq file names,  and some stats for that lane; including read length, total reads, count of good reads, and the percent of good reads.
 
  
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# To begin demultiplexing, run screen on mal or desired machine.
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==Trouble shooting==
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# cd new/runName/fastq/
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# Things to make sure before you begin
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# ~giardine/illumina/demultiplex.pl RUN_NAME sampleSheet.csv
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# 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.
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#*:~cathy/bin/line-ends<br />
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#*:Usage:  /afs/bx.psu.edu/home/cathy/bin/line-ends <target> <filename> > output <br />
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#*:where target = win, mac, or unix
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#*:Example: /afs/bx.psu.edu/home/cathy/bin/line-ends unix run26_SampleSheet.csv > run26_SampleSheet_endunix.csv
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Return to [[HLab:Main]]

Latest revision as of 14:56, 19 December 2014

HiSeq 2000

  1. Make sure sample sheet does not include quotes.
    • requires index sequence to only be six bases
  2. 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.
  3. cd output-dir
  4. On mal: (screen or) nohup make -j 4
  5. concat read1, read2 fastq files
  6. Put symlinks in production folder pointing to fastq files
  7. Copy data from illumina-9 to rawseq folder
  8. Copy reports and status files to runReports folder, make link in run table

NextSeq 500

  1. Copy data from learfan back to rawseq directory.
  2. Copy sample sheet to top directory of run folder, name must be SampleSheet.csv
    • requires all 7 bases of index in sample sheet
  3. 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)
  4. Make symlinks in fastq folder to rawseq Data/Intensities/BaseCalls
  5. Put symlinks in production folder pointing to fastq files

MiSeq

  1. rsync rawdata back to bx from makova-miseq-cache.
  2. Convert to fastq if necessary (similar to HiSeq)

HiSeq at Huck

  1. Get fastq files and Fastqc reports from ftp site (lab user name and password required).

Trouble shooting

  1. Things to make sure before you begin
  2. 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

Return to HLab:Main

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