/38_ZhuBO_RNAseq4_DKO

Primary LanguageR

38_ZhuBO_RNAseq4_DKO

Mapping using hisat2

Read lenght: 150bp

## example command
hisat2 -p 4 --summary-file hisat.summary  -x /home/lakhanp/database/Mouse/GRCm38.99/hisat2_index/Mus_musculus.GRCm38.99.dna.primary_assembly.chr.fa -1 /home/lakhanp/analysis/core_projects/38_ZhuBO_RNAseq4_DKO/raw_data/BZ_1_CRRA200002808-1a_HV3KTDSXX_L1_1.fq.gz -2 /home/lakhanp/analysis/core_projects/38_ZhuBO_RNAseq4_DKO/raw_data/BZ_1_CRRA200002808-1a_HV3KTDSXX_L1_2.fq.gz | samtools view -bS - | samtools sort  -O bam -o WT_1_hisat2.bam

Create BAM file index

for i in `cat sample_name.list`
do
cd $i
printf "samtools index %s_hisat2.bam
samtools flagstat %s_hisat2.bam > alignment.stats\n\n" $i $i >> generalJob.sh
cd ..
done

Run stringTie in estimation mode

for i in `cat sample_name.list`
do
cd $i
printf "##Run stringtie: just counting the transcripts and no assembly
stringtie %s_hisat2.bam -p 4 -e -B -G /home/lakhanp/database/Mouse/GRCm38.99/annotation/Mus_musculus.GRCm38.100.chr.gtf -o stringTie_%s/%s.gtf
error_exit \$?\n\n" $i $i $i >> generalJob.sh
cd ..
done