Hisat For loop in differential expression

[ZainabKamel]

INDEX=~/workdir/diff_exp/ref/ERCC92 we were fRUNLOG=runlog.txt READS_DIR=~/workdir/sample_data/ mkdir bam

for SAMPLE in HBR UHR; do for REPLICATE in 1 2 3; do R1=$READS_DIR/${SAMPLE}_Rep${REPLICATE}read1.fastq.gz R2=$READS_DIR/${SAMPLE}_Rep${REPLICATE}read2.fastq.gz BAM=bam/${SAMPLE}_${REPLICATE}.bam

    hisat2 $INDEX -1 $R1 -2 $R2 | samtools sort > $BAM
    samtools index $BAM
done

done

[ZainabKamel]

No input file and 0% reads because naming of files are different

[ZainabKamel]

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