:78 Function create_function() is deprecated [8192]
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diff --git a/README b/README index ccfbfe6..386bd06 100644 --- a/README +++ b/README @@ -454,13 +454,14 @@ showing the trend in use of working space. I) calling reads for genic regions (ORF) I.i) the following command will run the countReads.sh script using: - - 'data2/_1_MED1_INPUT_S25_L007_R1_001.fasta.gz' as the file with the INPUT reads - - 'data2/_3_MED1_IP_S27_L007_R1_001.fasta.gz' as the file with IP reads - - 'T_thermophila_June2014_assembly.fasta' as the reference genome for the T.thermophila organism - - 'T_thermophila_June2014.gff3' as the annotation file for the T.thermophila + - 'dataDIR/chipseq_INPUT_file.fasta.gz' as the file with the INPUT reads + - 'dataDIR/chipseq_IP_file.fasta.gz' as the file with IP reads + - 'REFfiles/T_thermophila_June2014_assembly.fasta' as the reference genome for the T.thermophila organism + - 'REFfiles/T_thermophila_June2014.gff3' as the annotation file for the T.thermophila - '/tmp/' as working space + - notice that 'dataDIR' and 'REFfiles' are the directories where the data is located and it can be given as absolute or relative paths - PATHtoRACSrepo/core/countReads.sh data2/_1_MED1_INPUT_S25_L007_R1_001.fastq.gz data2/_3_MED1_IP_S27_L007_R1_001.fastq.gz T_thermophila_June2014_assembly.fasta T_thermophila_June2014.gff3 /tmp/ + PATHtoRACSrepo/core/countReads.sh dataDIR/chipseq_INPUT_file.fastq.gz dataDIR/chipseq_IP_file.fastq.gz REFfiles/T_thermophila_June2014_assembly.fasta REFfiles/T_thermophila_June2014.gff3 /tmp/ In this case, beucase we haven't specfied the number of cores to use, the script will try to automatically detect the number of cores in the computer and @@ -473,21 +474,21 @@ parallel regions of the pipeline. Additionally it is using the system's 'time' command to time how long the pipeline takes to run. - time PATHtoRACSrepo/core/countReads.sh data2/_1_MED1_INPUT_S25_L007_R1_001.fastq.gz data2/_3_MED1_IP_S27_L007_R1_001.fastq.gz T_thermophila_June2014_assembly.fasta T_thermophila_June2014.gff3 /dev/shm/ 16 + PATHtoRACSrepo/core/countReads.sh dataDIR/chipseq_INPUT_file.fastq.gz dataDIR/chipseq_IP_file.fastq.gz REFfiles/T_thermophila_June2014_assembly.fasta REFfiles/T_thermophila_June2014.gff3 /dev/shm/ 16 II) Determination of InterGenic Regions (IGR) II.i) the following command will determine the intergenic regions, using: - - 'combinedTABLES_MED1-MED2' as the table which was determined in the ORF part of the pipeline - - 'dataset/T_thermophila_June2014.sorted.gff3' as the micro-organism reference genome file - - 'interGENs_MED1-MED2.csv' is the name of the table that the IGR part of the pipeline will + - 'FINAL.table.chipseq_INPUT_file-chipseq_IP_file' as the table which was determined in the ORF part of the pipeline; this file is located in the output subdirectory ORF_RACS_results-YYYYMMDD-HHMM + - 'REFfiles/T_thermophila_June2014.gff3' as the micro-organism reference genome file + - 'interGENs_chipseqExp_INPUTid-IPid.csv' is the name of the table that the IGR part of the pipeline will generate, ie. this will be the output of this part of the pipeline - 'samples.file' is a text file containing the name of the BAM output file, also generated when running the ORF part from RACS; they are usually named as alnDATASET_INDICATORS_ChIP_SXX_RY_ZZZ.fastq.gz-sorted.bam alnDATASET_INDICATORS_Input_SXX_RY_ZZZ.fastq.gz-sorted.bam - PATHtoRACSrepo/core/intergenic/det-interGenes.sh combinedTABLES_MED1-MED2 dataset/T_thermophila_June2014.sorted.gff3 interGENs_MED1-MED2.csv samples.file + PATHtoRACSrepo/core/intergenic/det-interGenes.sh FINAL.table.chipseq_INPUT_file-chipseq_IP_file REFfiles/T_thermophila_June2014.sorted.gff3 interGENs_chipseqExp_INPUTid-IPid.csv samples.file II.ii) we included a submission script in the 'hpc' directory, named "IGR-jobs_parallel.gnu", @@ -552,11 +553,11 @@ filters have to be specified; eg. For instance, the following command will select the micro-RNA for the Tetrahymena thermophila, - PATHtoRACSrepo/core/table.sh T_thermophila_June2014.gff3 PATHtoRACSrepo/core/defns/TT_mRNA.id + PATHtoRACSrepo/core/table.sh REFfiles/T_thermophila_June2014.gff3 PATHtoRACSrepo/core/defns/TT_mRNA.id or, the "genes" for the Oxytricha trifallax, - PATHtoRACSrepo/core/table.sh Oxytricha_trifallax_022112.gff3 PATHtoRACSrepo/core/defns/OXY_gene.id + PATHtoRACSrepo/core/table.sh REFfiles/Oxytricha_trifallax_022112.gff3 PATHtoRACSrepo/core/defns/OXY_gene.id IV.ii) ORF determination @@ -564,9 +565,9 @@ IV.ii) ORF determination information passed to the "table.sh" script as explained in the previous examples for the analysis of ORFs, - PATHtoRACSrepo/core/countReads.sh data2/_1_MED1_INPUT_S25_L007_R1_001.fastq.gz data2/_3_MED1_IP_S27_L007_R1_001.fastq.gz T_thermophila_June2014_assembly.fasta T_thermophila_June2014.gff3 /dev/shm/ 16 PATHtoRACSrepo/core/defns/TT_mRNA.id + PATHtoRACSrepo/core/countReads.sh dataDIR/chipseq_INPUT_file.fastq.gz dataDIR/chipseq_IP_file.fastq.gz REFfiles/T_thermophila_June2014_assembly.fasta REFfiles/T_thermophila_June2014.gff3 /dev/shm/ 16 PATHtoRACSrepo/core/defns/TT_mRNA.id - PATHtoRACSrepo/core/countReads.sh SRX483016_1.fastq.gz SRX483017_1.fastq.gz Oxytricha_trifallax_022112_assembly.fasta Oxytricha_trifallax_022112.gff3 /dev/shm/ 16 PATHtoRACSrepo/core/defns/OXY_gene.id + PATHtoRACSrepo/core/countReads.sh dataDIR/SRX483016_1.fastq.gz dataDIR/SRX483017_1.fastq.gz REFfiles/Oxytricha_trifallax_022112_assembly.fasta REFfiles/Oxytricha_trifallax_022112.gff3 /dev/shm/ 16 PATHtoRACSrepo/core/defns/OXY_gene.id where "SRX483017_1.fastq.gz" corresponds to the data for the ChIP-Seq run/experiment #1, and "SRX483016_1.fast1.gz" corresponds to the data for the @@ -578,7 +579,7 @@ solely difference that the script will try to automatically detect and use all the cores available in the computer; this is achieved by setting the 6th argument to "", which is needed when indicating the seventh argument: - PATHtoRACSrepo/core/countReads.sh SRX483016_1.fastq.gz SRX483017_1.fastq.gz Oxytricha_trifallax_022112_assembly.fasta Oxytricha_trifallax_022112.gff3 /dev/shm/ "" PATHtoRACSrepo/core/defns/OXY_gene.id + PATHtoRACSrepo/core/countReads.sh dataDIR/SRX483016_1.fastq.gz dataDIR/SRX483017_1.fastq.gz REFfiles/Oxytricha_trifallax_022112_assembly.fasta REFfiles/Oxytricha_trifallax_022112.gff3 /dev/shm/ "" PATHtoRACSrepo/core/defns/OXY_gene.id IV.iii) IGR determination @@ -586,7 +587,7 @@ IV.iii) IGR determination considerations other than using the "FINAL.table.*" file generated by the RACS' ORF tool. Eg. - PATHtoRACSrepo/core/intergenic/det-interGenes.sh FINAL.table.SRX483016_1-SRX483017_1 Oxytricha_trifallax_022112.gff3 interGENs_run1_OXY.csv sample.input + PATHtoRACSrepo/core/intergenic/det-interGenes.sh FINAL.table.SRX483016_1-SRX483017_1 REFfiles/Oxytricha_trifallax_022112.gff3 interGENs_run1_OXY.csv sample.input where the file "sample.input" contains the following files: