Description of parameters:
-o
output directory
-p
the number of threads to align reads (default used is 8)
-G
the path to the annotation file
/data/TOPHAT_Genome_Index/GRCm38.p6.genome is the path and prefix name of reference genome file
reads/filtered_reads/SRR5858228_1_trimmed.gz is the path to preprocessed and trimmed reads
Output The alignments are stored in BAM file format. Additionally, a text file is generated
indicating the alignment rate and the number of reads or pairs with multiple alignments.
Further, identified exon junctions, insertions, and deletions are stored in a separate BED
file.
STAR: STAR (Spliced Transcripts Alignment to a Reference) is a fast alignment
algorithm albeit having relatively higher memory requirements [39]. It is based on maximum mappable length approach that involves splitting individual reads into pieces or seeds
and identifying best segments that can be mapped for each seed (Fig. 11.4b). Next,
segments are stitched together and mapped using the genome sequence as an uncompressed
suffix array including information of splice sites (see Chap. 9, Sect. 9.2.3.1). The main
steps in alignment/mapping using STAR are described below:
Building/Exporting Reference Index STAR provides two options to either create a
custom genome index using suffix arrays or directly utilize available STAR references
indices. To include SJ annotation into the mapping process, a separate splice junction
reference file is required while constructing a customized reference index. Additionally, the
memory requirement for running STAR can be reduced by using a relatively sparser suffix
array that eventually reduces alignment speed. The reference index is created as follows:
Description of parameters:
--runThreadN
number of threads
--runMode
is set to genomeGenerate, which generates genome files
--genomeDir
the path to the output directory name
--genomeFastaFiles
the path to the genome fasta file
--sjdbGTFfile
the path to the annotation file
11 Design and Analysis of RNA Sequencing Data
155
-o
output directory
-p
the number of threads to align reads (default used is 8)
-G
the path to the annotation file
/data/TOPHAT_Genome_Index/GRCm38.p6.genome is the path and prefix name of reference genome file
reads/filtered_reads/SRR5858228_1_trimmed.gz is the path to preprocessed and trimmed reads
Output The alignments are stored in BAM file format. Additionally, a text file is generated
indicating the alignment rate and the number of reads or pairs with multiple alignments.
Further, identified exon junctions, insertions, and deletions are stored in a separate BED
file.
STAR: STAR (Spliced Transcripts Alignment to a Reference) is a fast alignment
algorithm albeit having relatively higher memory requirements [39]. It is based on maximum mappable length approach that involves splitting individual reads into pieces or seeds
and identifying best segments that can be mapped for each seed (Fig. 11.4b). Next,
segments are stitched together and mapped using the genome sequence as an uncompressed
suffix array including information of splice sites (see Chap. 9, Sect. 9.2.3.1). The main
steps in alignment/mapping using STAR are described below:
Building/Exporting Reference Index STAR provides two options to either create a
custom genome index using suffix arrays or directly utilize available STAR references
indices. To include SJ annotation into the mapping process, a separate splice junction
reference file is required while constructing a customized reference index. Additionally, the
memory requirement for running STAR can be reduced by using a relatively sparser suffix
array that eventually reduces alignment speed. The reference index is created as follows:
Description of parameters:
--runThreadN
number of threads
--runMode
is set to genomeGenerate, which generates genome files
--genomeDir
the path to the output directory name
--genomeFastaFiles
the path to the genome fasta file
--sjdbGTFfile
the path to the annotation file
11 Design and Analysis of RNA Sequencing Data
155