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Made snippet input- and output files more harmonised.

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This commit is contained in:
Hylke C. Donker
2021-02-22 13:18:18 +01:00
parent a2bc313515
commit f93596dd87
5 changed files with 57 additions and 36 deletions
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19
rnaseq/step3_align/snippet.sh
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@ -2,25 +2,26 @@
#
# Align reads against reference genome.
STORAGE="/groups/umcg-griac/tmp04/rawdata/$(whoami)/step3"
PROJECT_DIRECTORY="/groups/umcg-griac/tmp01/rawdata/$(whoami)/rnaseq"
# Store genome index in this location:.
GENOME_INDEX="${STORAGE}/genome_index"
GENOME_INDEX="${PROJECT_DIRECTORY}/step3/genome_index"
mkdir -p "${GENOME_INDEX}"
# Store the generated `Aligned.sortedByCoord.out.bam` in this dir.
ALIGNMENT_OUTPUT="${STORAGE}/alignment"
ALIGNMENT_OUTPUT="${PROJECT_DIRECTORY}/step3/alignment/"
mkdir -p "${ALIGNMENT_OUTPUT}"
# 1) Generate genome index.
#
# N.B.:
# - 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). An alternative
# cut-off is 150, for low-input methods. In general, refer back to the
# 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.
# - We're using gzip compressed reference data (--readFilesCommand zcat), i.e.,
# .gtf.gz and fa.gz. If not, you can remove the `zcat` flag.
# Storage location reference data (in this case on calculon).
REFERENCE_DATA="/groups/umcg-griac/prm02/rawdata/reference/genome"
# Storage location reference data (in this case on Gearshift).
REFERENCE_DATA="/groups/umcg-griac/prm03/rawdata/reference/genome"
GTF_FILE="${REFERENCE_DATA}/Homo_sapiens.GRCh38.100.gtf.gz"
FASTA_FILE="${REFERENCE_DATA}/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz"
@ -40,9 +41,9 @@ STAR \
# - We are assuming paired-end, gzip compressed (--readFilesCommand zcat) FastQ
# files.
# THe compressed paired-end FastQ's that we are aligning.
R1="sample1_R1.fastq.gz"
R2="sample1_R2.fastq.gz"
# The compressed, paired-end, FastQ's after trimming (step 2).
R1="${PROJECT_DIRECTORY}/step2/sample1_R1_paired.fastq.gz"
R2="${PROJECT_DIRECTORY}/step2/sample1_R2_paired.fastq.gz"
STAR \
--runThreadN 8 \