Generate "sam | bam" files from the quantification step

[JamalEH]

Dear Team,

In the user manual of Whippet it is stated the following regarding the generation of sam files: julia bin/whippet-quant.jl fwd_file.fastq.gz --sam > fwd_file.sam samtools view -bS fwd_file.sam > fwd_file.bam

Is this also valid in the case of paired-end RNA-seq datasets? or the command should be run as follows: julia bin/whippet-quant.jl fwd_file.fastq.gz rev_file.fastq.gz --sam > name_file.sam

Thank you in advance! Best regards, Jamal.