Hi
Recently, I encountered some problem.
I use the following code to get the bam file
hisat2 -p 46 -x ./1_index/99 --rna-strandness RF -1 ../0_archive/paired/${a}_R1.paired.fq.gz -2 ../0_archive/paired/${a}_R2.paired.fq.gz -S ./${a}.samsamtools view -@ 46 -bS ./${a}.sam > ./${a}.bamsamtools sort -@ 46 ./${a}.bam -T ./${a}.sorted -o ./${a}.sorted.bamsamtools index ${a}.sorted.bam
and then the following code to get the count file
htseq-count -f bam -i transcript_id -s reverse ${a}.sorted.bam ../1_data/gtf/99.gtf > ./${a}.count
and then the following code to get the TPM file
stringtie -p 48 -e ${a}.sorted.bam -G ../1_data/gtf/99.gtf -o ./outfile${a}.gtf -A ./${a}.abundance -C ./${a}_ref.gtf
However，When I check the CNAG_00001 gene, the count of CNAG_00001 is zero, but the TPM is 8 in abundance file
I upload the 1.count ,1.abundance file, part of 99.gtf file and part of bam file
Hi Recently, I encountered some problem. I use the following code to get the bam file
hisat2 -p 46 -x ./1_index/99 --rna-strandness RF -1 ../0_archive/paired/${a}_R1.paired.fq.gz -2 ../0_archive/paired/${a}_R2.paired.fq.gz -S ./${a}.samsamtools view -@ 46 -bS ./${a}.sam > ./${a}.bamsamtools sort -@ 46 ./${a}.bam -T ./${a}.sorted -o ./${a}.sorted.bamsamtools index ${a}.sorted.bamand then the following code to get the count file
htseq-count -f bam -i transcript_id -s reverse ${a}.sorted.bam ../1_data/gtf/99.gtf > ./${a}.countand then the following code to get the TPM file
stringtie -p 48 -e ${a}.sorted.bam -G ../1_data/gtf/99.gtf -o ./outfile${a}.gtf -A ./${a}.abundance -C ./${a}_ref.gtfHowever，When I check the CNAG_00001 gene, the count of CNAG_00001 is zero, but the TPM is 8 in
abundancefileI upload the
1.count,1.abundancefile, part of99.gtffile and part ofbamfileLooking forward your reply. file.zip