Hello, I am using Hisat2 for paired-end RNAseq, gene differential expression analysis. I am wondering can the sam files from Hisat2 directly used as input for HTseq, which I believe requires name sorted?
If not, should I convert as below?
hisat2 -x index -1 sample_R1.fastq -2 sample_R2.fastq -S sample.sam
samtools view -bS sample.sam > sample.bam
samtools sort -n sample.bam sample.sorted
samtools view -h -o sample _sort.sam sample.sorted.bam
htseq-count -m union -s no sample _sort.sam genes.gtf > sample _sort.readcount.txt
This takes quite a long time though… Is there a faster way? Thanks so much!
If not, should I convert as below?
hisat2 -x index -1 sample_R1.fastq -2 sample_R2.fastq -S sample.sam
samtools view -bS sample.sam > sample.bam
samtools sort -n sample.bam sample.sorted
samtools view -h -o sample _sort.sam sample.sorted.bam
htseq-count -m union -s no sample _sort.sam genes.gtf > sample _sort.readcount.txt
This takes quite a long time though… Is there a faster way? Thanks so much!
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