From 48b0ca75fc99eb9d74b46780a81cde7b3874b499 Mon Sep 17 00:00:00 2001 From: Federico Lopez Date: Tue, 29 Sep 2020 14:34:51 +0100 Subject: [PATCH] Delete input_amel.sh --- 01-quality_control/input_amel.sh | 119 ------------------------------- 1 file changed, 119 deletions(-) delete mode 100644 01-quality_control/input_amel.sh diff --git a/01-quality_control/input_amel.sh b/01-quality_control/input_amel.sh deleted file mode 100644 index 3ae82f4..0000000 --- a/01-quality_control/input_amel.sh +++ /dev/null @@ -1,119 +0,0 @@ -# I got cDNA A. mellifera genome from ENSEMBL Metazoa: -wget ftp://ftp.ensemblgenomes.org/pub/metazoa/release-46/fasta/apis_mellifera/cdna/Apis_mellifera.Amel_4.5.cdna.all.fa.gz - -# I download data for different tissues for foragers and queens from Jasper et al. 2015 -# I create a temporary (tmp) directory in scratch -ln -s ~/scratch tmp -# And copy there all the previously download files from -# https://www.ebi.ac.uk/ena/data/view/PRJNA243651 - -# All the data used in this project is now in: -~/db/rna/reads/Apis_mellifera -# That is: Manfredini et al. 2015, Liberti et al. 2015 (queens), Christen et al. 2018, Jasper et al. 2015 (workers). - -##FastQC: - -## required: -module load fastqc/0.11.9 - -### run quantifications -for name in *.fastq.gz; -do -fastqc "$name" -t 40; -done - -##STAR: - -##required: -module load star/2.7.0f - -#Create index: -mkdir star_amel_index - -STAR --runThreadN 6 \ ---runMode genomeGenerate \ ---genomeDir star_amel_index \ ---genomeFastaFiles ../input/Apis_mellifera.Amel_4.5.dna.toplevel.fa ---sjdbGTFfile ../input/Apis_mellifera.Amel_4.5.47.gtf ---sjdbOverhang 100 - - #paired end: -for FILE in ./*.1.fastq.gz - do - SRR_ID=$(basename $FILE .1.fastq.gz) - STAR --genomeDir ./star_amel_index \ - --runThreadN 14 \ - --readFilesIn ./${SRR_ID}".1.fastq.gz" ./${SRR_ID}".2.fastq.gz" \ - --outFileNamePrefix ./STAR_UTPUT/$SRR_ID \ - --readFilesCommand gunzip -c \ - --outSAMtype BAM SortedByCoordinate \ - --outSAMunmapped Within \ - --outSAMattributes Standard > ${SRR_ID}_star.log - done &! - - #single end: -for FILE in ./*.fastq.gz - do - SRR_ID=$(basename $FILE .fastq.gz) - STAR --genomeDir ./star_amel_index \ - --runThreadN 8 \ - --readFilesIn ./${SRR_ID}".fastq.gz" \ - --outFileNamePrefix ./STAR_UTPUT/$SRR_ID \ - --readFilesCommand gunzip -c \ - --outSAMtype BAM SortedByCoordinate \ - --outSAMunmapped Within \ - --outSAMattributes Standard > ${SRR_ID}_star.log - done &! - - -##QualiMap: - -##required: -module load qualimap/2.2.1 - -#I quantify with salmon to assess if data are strand-specific or not for a single sample from each study:# I ran it only for a single sample for each study included in the analyses. -salmon quant -t ./Apis_mellifera.Amel_4.5.dna.toplevel.fa -l A -a sample_1Aligned.sortedByCoord.out.bam -o salmon_quant -#all resulted as unstranded - -#paired-end: -for FILE in ../STAR/STAR_OUTPUT/jasper_2015/*.sortedByCoord.out.bam -do - BAM_ID=$(basename $FILE .sortedByCoord.out.bam) - qualimap rnaseq -bam $FILE -gtf Apis_mellifera.Amel_4.5.47.gtf -pe -outdir ../tm/qualimap/jasper_2015/$BAM_ID > ${BAM_ID}_star.log -done - -#single-end: -for FILE in ../STAR/STAR_SAM_OUTPUT/christen_2018/*.sortedByCoord.out.bam -do - BAM_ID=$(basename $FILE .sortedByCoord.out.bam) - qualimap rnaseq -bam $FILE -gtf Apis_mellifera.Amel_4.5.47.gtf -outdir ../tm/qualimap/christen_2018/$BAM_ID > ${BAM_ID}_star.log -done - -##Kallisto - -# Define reference file for Kallisto -kallisto_ref=tm/Amel_index - -## Generate kallisto-index: -./kallisto index -i $kallisto_ref input/Apis_mellifera.Amel_4.5.cdna.all.fa.gz - -### Create a directory for the results -mkdir tmp/kallisto_output - -#single-end: -for FILE in *.fastq.gz - do - OUTPUT_ID=$(basename $FILE .fastq.gz) - ./kallisto quant --index=tm/Amel_index --bias --bootstrap-sample=100 \ - --output-dir=kallisto_output/$OUTPUT_ID \ - --threads=10 --single -l 300 -s 20 input/renamed/${OUTPUT_ID}.fastq.gz > ${OUTPUT_ID}__kallisto_run.log - done - - #paired-end: - for FILE in *.1.fastq.gz - do - OUTPUT_ID=$(basename $FILE .1.fastq.gz) - ./kallisto quant --index=tm/Amel_index --bias --bootstrap-sample=100 \ - --output-dir=kallisto_output/$OUTPUT_ID \ - --threads=10 input/renamed/${OUTPUT_ID}".1.fastq.gz" input/renamed/${OUTPUT_ID}".2.fastq.gz" > ${OUTPUT_ID}_kallisto_run.log - done \ No newline at end of file