title: RNA-Seq of human A549 infected with IAV SC35M NS1 184-188 mutant
design: The library preparation of the total RNA was performed with the NEBNext Ultra II RNA directional Kit and single read sequencing was performed using a NextSeq 500 System with a read length of 75 bp. Using a molecular barcode, the samples will be demultiplexed (bcl2fastq2) to fastq data and quality controlled (FastQC). Trimmomatic will be used for adapter trimming and read filtering1. The resulting reads were aligned to the Ensembl GRCh38 reference genome using Hisat22. The aligned reads were sorted using samtools3. The sorted and aligned reads were counted into genes using htsec-counts 4a. The test for differential expression were performed using the r-package deseq25a.