Files added: RNAseq_pipeline, feature_filter.py

README.md

@@ -1,78 +1,21 @@
 # RNAseq
 The Gresham Lab RNAseq pipeline
 
-Version 1.0 - 10/18/2017
+Version 2.0 - 10/31/2017
 
 Usage: The intent of this pipeline is to standardize RNA-seq alignments 
-for the Gresham lab and to make the most of the HPC environment.
+for the Gresham lab and to make the most of the HPC environment. v2.0 
+intorduced a python wrapper to handle the generation of the SBATCH bash
+file. 
 
-## To Use:
+Please use the '-h' or '-help' commands to access details about 
+command line arguments and examples command lines.
 
-A. Necessary steps: 
-
-	1. Define the SBATCH array size (line 2):
-		#SBATCH --array=0-N
-		Purpose: SBATCH needs to launch a number of runs equal 
-		to the number of fastq files that need to be processed. This 
-		command dictates the number of runs to launch. 
-		Modify: Change the variable 'N' to the number of fastq files
-		contained in the DIR directory. Note the zero indexing, if you have 
-		two fastq files, N = 1 and the command is #SBATCH --array=0-1.
-
-	2. Define run configuration (line 26-28):
-		a. The name of the analysis (line 26):
-		analysisName="N"
-		Purpose: Name defines output folder name
-		b. Is the library Paired End (line 27):
-		isPE=N
-		Purpose: Paired end and single end libraries require distinct
-		operations, this value define the operations applied to your library. 
-		Modify: If paired end (PE) set 'N' to 1, if single end (SE) set 'N' to 0.
-		c. Does the library have UMIs (line 28):
-		isUMI=N
-		Purpose: UMI labelled libraries require an additional step to
-		to demultiplex, this values dictates whether or not that occurs. 
-		Modify: If UMIs were used in library prep, set 'N' to 1, else 
-		set 'N' to 0.
+	python RNAseq_pipeline.py -h    
 
-	3. Define directory containing fastq files to process (line 34):
-		DIR='N'
-		Purpose: Directory conatins fastq files to process.
-		Modify: Set directory 'N' to the location of your files.
-		NOTE: Current sbatch capacities have an upper limit of runs per 
-		individual user. If you encouter an 'excessive runs' error you may 
-		need to split your files into two seperate directories.
+----------------------------------------------------------------------
+Please report all issues and bugs to the GreshamLab github page:
+https://github.com/GreshamLab/RNAseq/issues
 
-	4. Define compression state (line 56 - 57):
-		#FILES=($(ls $DIR/*fastq.gz | perl -pe 's/^.+n0\d_(.+)\.fastq\.gz/$1/g' | sort | uniq))
-		FILES=($(ls $DIR/*fastq | perl -pe 's/^.+n0\d_(.+)\.fastq/$1/g' | sort | uniq))
-		Purpose: Command collects the filenames of files with a defined 
-		file extension, either fastq.gz or fastq.
-		Modify: If the files have the gz extension (ie. *.fastq.gz),
-		uncomment line 56 and comment line 57. If the files do not have the 
-		gz extension (ie. *.fastq), comment line 56 and uncomment line 57.
-
-B. Optional Modifications:
-
-	1. Reference Genome (line 35):
-		hisat_ref='N'
-		Purpose: Defines genome to align against.
-		Modify: Set 'N' to point to a valid genome. The default genome
-		has spike in sequences (BAC, CEL, ERCC) already present.
-
-	2. Genome Annotation (line 37):
-		gff='N'
-		Purpose: Defines annotation file for alignment.
-		Modify: Set 'N' to point to a valid 'gff' file. NOTE: Older 
-		annotation formats (eg. 'gtf', 'gff2') are not supported. 
 
-
-##
-#	Please submit issues to:
-#		https://github.com/GreshamLab/RNAseq/issues
-#	--------------------------------------------------- 
-##	
-
-## Features for future versions:
-	1. General interface python wrapper.
-
+MIT License Copyright (c) 2017 David Gresham