HIV latency transcriptomics of resting CD4+ T cells

The multiqc report highlighted potential issues with sample and/or library prep. A large proportion of reads were < 150bp read length (Illimina MiSeq) which seemed to result in negative 'Inner Distance'. Slight RNA degradation was also detected on the Gene Body Coverage graph. For the 'Latent' sample Jon noted that based on the complexity curve and the FastQC quality scores that there is a 'lot of incorrectly called bases along the length of the reads in the latent sample. Luckily, because this low quality is fairly uniform across the reads the alignment scores seem to be ok. So that sample is probably still good for expression analysis, but I wouldn’t trust it for any variant calling'. The multiqc report and the gene count matrix (which is very sparse) was sent to Walter, who agreed that they were having trouble with library prep and sequencing depth.