:78 Function create_function() is deprecated [8192]
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diff --git a/README b/README index 38f9bce..ccfbfe6 100644 --- a/README +++ b/README @@ -2,7 +2,7 @@ RACS: Rapid Analysis of ChIP-Seq data for contig based genomes ==== -------------------------------------------------------- These tools are a series of scripts developed to facilitate the analysis -of ChIP-Seq data and has been applied to the organism T. thermophila. +of ChIP-Seq data and has been applied to the organism Tetrahymena thermophila. === Content === @@ -23,6 +23,8 @@ of ChIP-Seq data and has been applied to the organism T. thermophila. - Downloading datasets - Comparing RACS results to MACS +* Notes about the use of RAMdisk and storage space as "working space" + * Examples * Citation & References @@ -385,10 +387,72 @@ More concrete examples and uses are presented in the examples section below. ------------------------------------------------------------------------------- +* Notes about the use of RAMdisk and storage space as "working space" + +When using the main script for counting reads, the user has the ability of +indicating whether to use a faster 'working space' than traditional spinning +disks (ie. HDD) such as memory (ie. RAMdisk) or a solid state devive (SSD). +In general, utilizing RAMdisk or SSDs, would result in a speed-up of roughly +10 to 30%, depending on hardware specifications and the size of the dataset +to be analyzed. +The larger the dataset the more IO operations that would be needed, hence +larger datasets would benefit the most of this. +This is of course, assuming that the data and subsequent auxiliary files +created during the analysis will fit in ``memory''. If that is not the case +then depending on the system and how ti is configured may result in decremental +performance (e.g. some computer will swap --i.e. start using traditional HDD +space--) or even crash (for instance, is common in many HPC clusters to do not +allow for swapping techniques). +Differences in performance among SSD vs RAMdisk, are almost negligible, again +depending on hardware specs, this can be upmost of the order of few +percentages. +Finally, it should be noticed that by using RAMdisk (i.e. memory) as a working +space, users will reduce the overall computational time, however this is will +ultimately depend upon the amount of memory available as this technique will +increase the utilization of RAM. +As a general estimate, at the moment of running the pipeline, users might +estimate the amount of memory needed by one order of magnitude larger (i.e. x +10) than the size of the dataset to be processed. + + +The following plot represents the typical behaviour in storage use in the +"working space" area during a typical run of RACS. +The vertical axis represents the size used in the 'working space' in units +of the total size of the initial data (INPUT and IP files, plus reference +files --gff3 and fasta files--). +Ie. a value of 8, means 8 times the original size of the initial data. +The horizontal axis is runtime in seconds, and the '*' represents data points +showing the trend in use of working space. + + + 9 +-+---------+-----------+-----------+----------+-----------+---------+-+ + + + + + + + + + 8 +-+ **** +-+ + | ****** ************ | + 7 +-+ *** ** * +-+ + | ******* * | + 6 +-+ ****** * +-+ + | * * | + 5 +-+ * * +-+ + | ** * | + | * * | + 4 +-+ ** * +-+ + | ************ * | + 3 +-+ * * +-+ + | ** * | + 2 +-+ * * +-+ + | *** * | + 1 **************** * +-+ + * + + + + + * + + 0 *-+---------+-----------+-----------+----------+-----------+-**------+-+ + 0 500 1000 1500 2000 2500 3000 + + +------------------------------------------------------------------------------- * EXAMPLES -I) calling peaks for ORF +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