Read_Mapping - LappalainenLab/RNApipeline GitHub Wiki

Basic Usage

The Read_Mapping handler aligns trimmed FASTQs using STAR. This script cannot generate a STAR index for the reference FASTA file on its own. Before running this handler, please ensure you've generated a STAR index for your reference genome.

To run Read_Mapping, all common and handler-specific variables must be defined within the configuration file. Once the variables have been defined, Read_Mapping can be submitted to a job scheduler with the following command (assuming that you are in the directory containing RNApipeline):

./main.sh Read_Mapping proj.conf

Handler-Specific Variables

The following are a list of variables that need to be defined within the configuration file. In addition to the handler-specific variables, all common variables must be defined.

Variable	Function
`RM_QSUB`	QSub settings for batch submission
`TRIMMED_LIST`	A list of adapter-trimmed or quality-trimmed samples to read map. This will be `${OUT_DIR}/Sequence_Trimming/${PROJECT}_trimmed.txt` if using Sequence_Trimming
`FORWARD_TRIMMED`	Shared suffix for forward reads. This will be `_forward_paired.fastq.gz` if using Sequence_Trimming
`REVERSE_TRIMMED`	Shared suffix for reverse reads. This will be `_reverse_paired.fastq.gz` if using Sequence_Trimming
`SINGLES_TRIMMED`	Shared suffix for single reads. This will be `_trimmed.fastq.gz` if using Sequence_Trimming
`REF_IND`	Directory with STAR reference index for `REF_GEN`

Note: If running single-end samples, leave FORWARD_TRIMMED and REVERSE_TRIMMED filled with values that do not match your samples. If running paired-end samples, leave SINGLES_TRIMMED filled with values that do not match your samples.

Output

Read_Mapping will output an aligned SAM file for each sample.

In addition, a list of all aligned SAM files will be generated for use with other handlers. The full file path to this list will be ${OUT_DIR}/Read_Mapping/${PROJECT}_Mapped.txt

Dependencies