Hi guys, I am currently working on paired-end RNA-seq data. I am running samtools using the following script for single ends, but I am not sure it is correct for paired-end, specially the part I use to get uniq.bam file.
samtools view -bS s1sequence.sam.gz > s1sequence.bam
samtools view -bq 1 s1sequence.bam > s1uniq.bam
samtools sort s1uniq.bam s1uniq.sorted
samtools index s1uniq.sorted.bam
samtools mpileup -vcf wg.fa s1uniq.sorted.bam > s1.pileupraw
Do you know if it is correct for paired-ends? I am a beginner so any advise is more than welcome! Thank you very much in advance!