gmap
Link to section 'Introduction' of 'gmap' Introduction
Gmap is a genomic mapping and alignment program for mRNA and EST sequences.
For more information, please check its website: https://biocontainers.pro/tools/gmap and its home page: http://research-pub.gene.com/gmap/.
Link to section 'Versions' of 'gmap' Versions
- 2021.05.27
- 2021.08.25
Link to section 'Commands' of 'gmap' Commands
- atoiindex
- cmetindex
- cpuid
- dbsnp_iit
- ensembl_genes
- fa_coords
- get-genome
- gff3_genes
- gff3_introns
- gff3_splicesites
- gmap
- gmap.avx2
- gmap_build
- gmap_cat
- gmapindex
- gmapl
- gmapl.avx2
- gmapl.nosimd
- gmap.nosimd
- gmap_process
- gsnap
- gsnap.avx2
- gsnapl
- gsnapl.avx2
- gsnapl.nosimd
- gsnap.nosimd
- gtf_genes
- gtf_introns
- gtf_splicesites
- gtf_transcript_splicesites
- gvf_iit
- iit_dump
- iit_get
- iit_store
- indexdb_cat
- md_coords
- psl_genes
- psl_introns
- psl_splicesites
- sam_sort
- snpindex
- trindex
- vcf_iit
Link to section 'Module' of 'gmap' Module
You can load the modules by:
module load biocontainers
module load gmap
Link to section 'Example job' of 'gmap' Example job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run Gmap on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 4
#SBATCH --job-name=gmap
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers gmap
gmap_build -d Cmm -D Cmm genome.fasta
gmap -d Cmm -t 4 -D ./Cmm cdna.fasta > gmap_out.txt
gmap_build -d GRCh38 -D GRCh38 Homo_sapiens.GRCh38.dna.primary_assembly.fa
gsnap -d GRCh38 -D ./GRCh38 --nthreads=4 SRR16956239_1.fastq SRR16956239_2.fastq > gsnap_out.txt