index using gff3 file chromosome 15 and Alignment using for loop

[Naiera13]

INDEX="/home/hp/Desktop/Project/chromosome15/Homo_sapiens.GRCh38.99.chromosome.15.gff3/" RUNLOG=runlog.txt READS_DIR="/home/hp/Desktop/Project/" mkdir bam for SAMPLE in hs_T47D_shCTRL_RNAseq_rep hs_T47D_shNR2F2_RNAseq_rep; do for REPLICATE in 1 2; do R=$READS_DIR/${SAMPLE}${REPLICATE}*.fastq.gz; BAM=bam/${SAMPLE}${REPLICATE}.bam; hisat2 $INDEX -U $R | samtools sort > $BAM; samtools index $BAM; done; done GTF="/home/hp/Desktop/Project/Chromosome15/Homo_sapiens.GRCh38.99.chromosome.15.gff3" featureCounts -a $GFF3 -g Name -o counts.txt bam/hs_T47D_shCTRL_RNAseq_rep.bam bam/hs_T47D_shNR2F2_RNAseq_rep.bam

[Naiera13]

cat counts.txt | cut -f 1,7-10 > simple_counts.txt cat simple_counts.txt | Rscript deseq1.r 2x2 > results_deseq1.tsv cat results_deseq1.tsv | awk ' $8 < 0.05 { print $0 }' > filtered_results_deseq1.tsv cat filtered_results_deseq1.tsv | Rscript draw-heatmap.r > hisat_output.pdf

[Naiera13]

hisat_output (1).pdf