Difference between revisions of "RNASeq: Obtaining read counts"
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Read counting may be CPU-intensive, depending on the size of the BAM file(s) used. It is thus recommended to run this process as a job script on Abel. Such a job script must first load the R module on Abel, subsequently executing an R script containing the read-counting R code. Such a job script may look like: | Read counting may be CPU-intensive, depending on the size of the BAM file(s) used. It is thus recommended to run this process as a job script on Abel. Such a job script must first load the R module on Abel, subsequently executing an R script containing the read-counting R code. Such a job script may look like: | ||
<div style="line-height:90%; background-color: LightGray; border-style: solid; border-width:1px; font-family:courier new,courier,monospace;"> | <div style="line-height:90%; background-color: LightGray; border-style: solid; border-width:1px; font-family:courier new,courier,monospace;"> | ||
− | #!/bin/bash | + | <nowiki>#</nowiki>!/bin/bash |
− | #SBATCH --job-name=my_R_script_name | + | <nowiki>#</nowiki>SBATCH --job-name=my_R_script_name |
− | #SBATCH --account=myAccountName | + | <nowiki>#</nowiki>SBATCH --account=myAccountName |
− | #SBATCH --time=48:00:00 | + | <nowiki>#</nowiki>SBATCH --time=48:00:00 |
− | #SBATCH --mem-per-cpu=3500M | + | <nowiki>#</nowiki>SBATCH --mem-per-cpu=3500M |
− | #SBATCH --nodes=1 | + | <nowiki>#</nowiki>SBATCH --nodes=1 |
− | #SBATCH --ntasks-per-node=1 | + | <nowiki>#</nowiki>SBATCH --ntasks-per-node=1 |
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− | module load R | + | module load R |
R CMD BATCH /path/to/Rscript.R | R CMD BATCH /path/to/Rscript.R | ||
</div> | </div> |
Latest revision as of 12:41, 28 May 2015
Read counting implies counting the number of reads that map inside a specific annotation feature. The tutorials listed here demonstrate read counting as part of differential gene expression using the R library DESeq/DESeq2. Alternatively, reads may be counted with the python program HTSeq-count, see the manual for instructions (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html).
Read counting may be CPU-intensive, depending on the size of the BAM file(s) used. It is thus recommended to run this process as a job script on Abel. Such a job script must first load the R module on Abel, subsequently executing an R script containing the read-counting R code. Such a job script may look like:
#!/bin/bash
#SBATCH --job-name=my_R_script_name
#SBATCH --account=myAccountName
#SBATCH --time=48:00:00
#SBATCH --mem-per-cpu=3500M
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
source /cluster/bin/jobsetup
module load R
R CMD BATCH /path/to/Rscript.R