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====Pipeline A.==== *This pipeline uses Tophat2 and Cufflink2. *We use one script to submit jobs for all samples in one folder, one job per sample. Here is how to start the job. # First, copy the job submission script to your own path, such as your HOME/bin cp /home/k4zhang/bin/submit_tophat_jobs.pl MY_HOME/bin # Next edit this script, replace the email address "kun.zhang.ucsd@gmail.com" with your own address. # This only need to be done once. # As a rehearsal, you can copy two test data sets to your own folder. cp -r /home/k4zhang/my_oasis_tscc/test_data MY_FOLDER # Now you can change to this folder. cd MY_FOLDER # Then you can submit all the jobs to process the samples in this folder. # For human data, replace mm10 with hg19. submit_tophat_jobs.pl mm10 # To check the status, use qstat. # You should also receive emails when the jobs are started or completed. qstat | grep YOUR_USER_NAME # The results are in tophat_xxx folder (one folder per sample). # After tophat mapping and cufflink quantification, the downstream analyses # are typically done on genome-miner, because it is more interactive and # less time consuming. For this, use sftp or scp to transfer all # tophat_xxx folders to genome-miner # To quickly get an overview of mapping stats and number of transcripts called, # run the following script within the GROUP_DATA_DIR that contains all tophat_xxx folders. /home/kunzhang/RNAseq/SCAP/get_mapping_stats.pl GROUP_DATA_DIR > group_name_mapping_stats.txt
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