Create Mapping Indices

Before we can perform NGS read mapping, we will create the genome indices using the genome FASTA file as input. You can re-use these indices in all your future RnA-seq mapping. However, if you wish to map to a different genome build/assembly, you have to re-run this step using different genome sequences and save the indices in a different directory.

Here, we will create indices for STAR and RSEM.



STAR --runMode genomeGenerate --genomeDir path_to_genomedir --genomeFastaFiles reference_fasta_file(s)


cd ~/LSLNGS2015
mkdir GENOME_data/star

STAR --runThreadN 40 --runMode genomeGenerate --genomeDir GENOME_data/star \
--genomeFastaFiles GENOME_data/Homo_sapiens.GRCh38.dna.primary_assembly.fa \
--sjdbGTFfile GENOME_data/Homo_sapiens.GRCh38.86.gtf

Resource usage

ALPS Queue Name CPU Time Max Memory Duration
128G 51610.02 sec. 31 GB 1 hour 15 minutes 6 seconds


--runThreadN defines the number of threads to be used for genome generation.

--runMode genomeGenerate directs STAR to run genome indices generation job.

--genomeDir path to the directory where the genome indices are stored. This directory has to be created (with mkdir) before STAR run and needs to writing permissions. The file system needs to have at least 100GB of disk space available for a typical mammalian genome.

--genomeFastaFiles one or more FASTA files with the genome reference sequences.

--sjdbGTFfile path to the transcript annotation in the standard GTF format.

Take a look at the STAR indices generated

ls -la ~/LSLNGS2015/GENOME_data/star

-rw-rw-r-- 1 ycl6 ycl6        1200 Oct 25 10:32 chrLength.txt
-rw-rw-r-- 1 ycl6 ycl6        3123 Oct 25 10:32 chrNameLength.txt
-rw-rw-r-- 1 ycl6 ycl6        1923 Oct 25 10:32 chrName.txt
-rw-rw-r-- 1 ycl6 ycl6        2129 Oct 25 10:32 chrStart.txt
-rw-rw-r-- 1 ycl6 ycl6    41854837 Oct 25 11:22
-rw-rw-r-- 1 ycl6 ycl6    16985258 Oct 25 11:22
-rw-rw-r-- 1 ycl6 ycl6      928822 Oct 25 11:22
-rw-rw-r-- 1 ycl6 ycl6  3208868819 Oct 25 11:27 Genome
-rw-rw-r-- 1 ycl6 ycl6         645 Oct 25 10:32 genomeParameters.txt
-rw-rw-r-- 1 ycl6 ycl6 24881828956 Oct 25 11:29 SA
-rw-rw-r-- 1 ycl6 ycl6  1565873619 Oct 25 11:29 SAindex
-rw-rw-r-- 1 ycl6 ycl6    10235563 Oct 25 11:22 sjdbInfo.txt
-rw-rw-r-- 1 ycl6 ycl6     8020752 Oct 25 11:22
-rw-rw-r-- 1 ycl6 ycl6     8019182 Oct 25 11:22
-rw-rw-r-- 1 ycl6 ycl6    11688566 Oct 25 11:22



rsem-prepare-reference [options] reference_fasta_file(s) reference_name


cd ~/LSLNGS2015
mkdir GENOME_data/rsem

rsem-prepare-reference --gtf GENOME_data/Homo_sapiens.GRCh38.86.gtf \ 
GENOME_data/Homo_sapiens.GRCh38.dna.primary_assembly.fa GENOME_data/rsem/GRCh38

Resource usage

ALPS Queue Name CPU Time Max Memory Duration
48G 140.03 sec. 2 GB 2 minutes and 26 seconds


--gtf option specifies path to the gene annotations (in GTF format), and RSEM assumes the FASTA file contains sequence of a genome. If this option is off, RSEM will assume the FASTA file contains the reference transcripts. The name of each sequence in the Multi-FASTA files is its transcript_id.

Take a look at the RSEM indices generated

ls -la ~/LSLNGS2015/GENOME_data/rsem

-rw-rw-r-- 1 ycl6 ycl6       696 Oct 25 08:12 GRCh38.chrlist
-rw-rw-r-- 1 ycl6 ycl6    393402 Oct 25 08:12 GRCh38.grp
-rw-rw-r-- 1 ycl6 ycl6 297970512 Oct 25 08:12 GRCh38.idx.fa
-rw-rw-r-- 1 ycl6 ycl6 297970512 Oct 25 08:12 GRCh38.n2g.idx.fa
-rw-rw-r-- 1 ycl6 ycl6 318104358 Oct 25 08:12 GRCh38.seq
-rw-rw-r-- 1 ycl6 ycl6 135696331 Oct 25 08:12 GRCh38.ti
-rw-rw-r-- 1 ycl6 ycl6 297970512 Oct 25 08:12 GRCh38.transcripts.fa

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