RECLU

[…] were mapped to rat reference genomes using the tophat2 software after discarding the ribosomal and non-a/c/g/t base-containing rnas []. for tag clustering, the cage-tag 5’-coordinates were input for reclu clustering, with a maximum irreproducible discovery rate (idr) of 0.1 and a minimum tags per million (tpm) value [], followed by differential expression and motif discovery analyses. the r […]

[…] cage tags were mapped to the mouse mm9 genomes using bwa software (v0.5.9) after discarding ribosomal or non-a/c/g/t base-containing rnas. for tag clustering, cage-tag 5′ coordinates were input for reclu clustering, with a maxmum irreproducible discovery rate of (idr) 0.1 and minimum tags per million (tpm) value of 0.1 [, ], genes were filtered into the rb inactivation signature if their tpm […]

[…] enough for further analyses (table ). then, profiling differentially expressing genes (peaks in rna sequence mapped to the reference genome) between experimental groups was obtained by a pipeline, reclu []. here, the reclu pipeline extracted two types of clusters, top peaks and bottom ones []. briefly, top peaks or bottom ones represent the narrowest or broadest reproducible peaks in an rna […]

[…] respectively. the remaining reads were mapped to s. pombe reference genome using bwa []. cage read clustering, differential gene expression analysis and motif discovery were performed by reclu ver3.1 pipeline (http://cell-innovation.nig.ac.jp/wiki2/tiki-index.php?page=p000001286), integrated into maser (national institute of genetics; https://cell-innovation.nig.ac.jp/index_en.html) […]