Error in for loop of Hisat2 in differential expression

[DrHudaAbuBakr]

we started to work in for loop: INDEX=~/Desktop/PROJECT/Hisat/hisat_align/Homo_sapiens.GRCH.38 RUNLOG=runlog.txt READS_DIR=~/Desktop/PROJECT/ mkdir bam

for SAMPLE in hs_T47D_shCTRL_RNAseq hs_T47D_shNR2F2_RNAseq; do for REPLICATE in 1 2 ; do file_name=$READS_DIR/${SAMPLE}Rep${REPLICATE}*.fastq.gz BAM=bam/${SAMPLE}${REPLICATE}.bam

    hisat2 $INDEX -U $file_name | samtools sort > $BAM
    samtools index $BAM
done

done

[ZainabKamel]

No input file and 0% reads

[Naiera13]

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