Mitochondrial dysfunction drives progression from acute to Long COVID

We used GRCh38 primary assembly reference genome (Ensembl release 110) and GENCODE primary assembly annotation (release 44) as the basis for sequence alignment and quantification. We used Trim Galore (version 0.6.10) for quality and adapter trimming on the FASTQ files. After trimming, we aligned the FASTQ files to the reference genome using STAR (version 2.7.11a). We provided STAR the “TranscriptomeSAM” setting to translate the alignments into transcript coordinates in an aligned BAM file. We used these BAM files to obtain quantifications using Salmon (version 1.10.1) subsequently using the gene-level counts from Salmon for downstream analyses. This workflow is publicly available from our GitHub repository at https://github.com/BioDepot/LongCOVID-RNAseq.