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Tailored storage locations to calculon.

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Hylke C. Donker 2021-02-11 10:47:21 +01:00
parent ef4a25f54b
commit d71460a7dd
1 changed files with 12 additions and 9 deletions
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21
rnaseq/step3_align/snippet.sh
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@ -2,7 +2,7 @@
# #
# Align reads against reference genome. # Align reads against reference genome.
STORAGE="/groups/umcg-griac/tmp01/rawdata/$(whoami)/step3" STORAGE="/groups/umcg-griac/tmp04/rawdata/$(whoami)/step3"
# Store genome index in this location:. # Store genome index in this location:.
GENOME_INDEX="${STORAGE}/genome_index" GENOME_INDEX="${STORAGE}/genome_index"
mkdir -p "${GENOME_INDEX}" mkdir -p "${GENOME_INDEX}"
@ -16,19 +16,22 @@ mkdir -p "${OUTPUT}"
# - We're assuming a read size of 100 bp (--sjdbOverhang 100). Refer back to the # - We're assuming a read size of 100 bp (--sjdbOverhang 100). Refer back to the
# previous quality control steps if you are unsure about the size. In case of # previous quality control steps if you are unsure about the size. In case of
# reads of varying length, the ideal value is max(ReadLength)-1. # reads of varying length, the ideal value is max(ReadLength)-1.
# - We're using gzip compressed reference data (--readFilesCommand zcat), i.e.,
# .gtf.gz and fa.gz. If not, you can remove the `zcat` flag.
# Where the reference data is stored. # Storage location reference data (in this case on calculon).
REFERENCE_DATA="/groups/umcg-griac/prm02/rawdata/reference/genome" REFERENCE_DATA="/groups/umcg-griac/prm02/rawdata/reference/genome"
GTF_FILE="${REFERENCE_DATA}/Homo_sapiens.GRCh38.100.gtf" GTF_FILE="${REFERENCE_DATA}/Homo_sapiens.GRCh38.100.gtf.gz"
FASTA_FILE="${REFERENCE_DATA}/Homo_sapiens.GRCh38.dna.primary_assembly.fa" FASTA_FILE="${REFERENCE_DATA}/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz"
STAR \ STAR \
--runThreadN 8 \ --runThreadN 8 \
--runMode genomeGenerate \ --runMode genomeGenerate \
--sjdbOverhang 100 \ --readFilesCommand zcat \
--genomeFastaFiles ${FASTA_FILE} \ --sjdbOverhang 100 \
--sjdbGTFfile ${GTF_FILE} \ --genomeFastaFiles ${FASTA_FILE} \
--genomeDir ${GENOME_INDEX} --sjdbGTFfile ${GTF_FILE} \
--genomeDir ${GENOME_INDEX}
# 2) Do the actual alignment. # 2) Do the actual alignment.