*4.7. Assembly of LINC01133 Isoforms Expressed in the 12Z Cell Line*

Aligned reads from the genomic positions chr1:159955239-15998963, were extracted using Samtools for all downstream analyses [56]. For that region, read coverage was calculated using bam2wig (v4.0.0) (https://github.com/MikeAxtell/bam2wig) accessed on 3 December 2020. Read coverage at each informative genomic position was normalized for sequencing depth and averaged over all control siRNA transfected and knockdown *LINC01133a* siRNA samples. Transcript assembly was performed using Cufflinks (v2.2.1) [57] with the parameter: -F 0.05. Note that for transcript assembly only the control siRNA samples were used and the resulting GTF files were merged using Cuffmerge to obtain the final *LINC01133* annotation.
