cleanUpdTSeq

cleanUpdTSeq is a software tool to enhance the analysis of mRNA isoforms with alternative polyadenylation (poly(A)) sites, a feature prevalent in eukaryotic genes that plays a crucial role in regulating numerous biological processes. cleanUpdTSeq is specifically aimed at improving the accuracy and efficiency of genome-wide poly(A) site identification and quantification of 3' mRNA isoform abundance, leveraging high-throughput sequencing technologies.

This software addresses nonspecific sequence reads commonly encountered in poly(A) site identification due to internal priming. This technical issue can significantly compromise the quality of the sequencing data. By employing a modified protocol of the 3'READS (3' region extraction and deep sequencing) method, cleanUpdTSeq effectively minimizes these nonspecific reads, ensuring a higher percentage of sequence reads are directly relevant for accurate poly(A) site detection.