proTRAC

[…] nd 137 hairpins which clustered into 70 groups (102 unique mature miRNAs) were selected which met our criterion, these were designated as novel X. laevis miRNAs. piRNA clustering and analysis we used probabilistic tracking and analysis of clusters (ProTRAC) []. […]

[…] ismatches allowed and were used to calculate TE-specific ping-pong Z-score and distribution of reads along the consensi.Probabilistic piRNA cluster calling was done with TBr2_duster.pl/sRNAmapper.pl/ proTRAC_2.1.2.pl pipeline by Rosenkranz and Zischler [, ] with proTRAC parameters as follows: -pdens 0.05 -1Tor10A 0.1 -1Tand10A 0.1 -clstrand 0.5 -clsplit 0.05. Finally, a list of 1299 of human piRNA […]

[…] e most piRNAs are derived from genomic piRNA clusters [–], the second class utilizes the information on clustering locus for piRNA detection. Among the approaches based on clustering locus of piRNAs, proTRAC [] can identify piRNA clusters and piRNAs from a small RNA-seq dataset through a probabilistic analysis of mapped sequence reads. Furthermore, piClust [] uses a density-based clustering method […]

[…] piRNA cluster detection was performed on Nematostella piRNAs using the proTRAC pipeline version 2.1 with the options protrac_nv (Supplemental Table S3) for each developmental stage. Clusters were then merged using the bedtools suite, resulting in 457 clusters. Unassigned […]

[…] ware.html) was used to assign read counts of multiple mapping sequences according to estimated local transcription rates based on uniquely mapping sequences.piRNA cluster detection was performed with proTRAC version 2.1 [, ], imposing a piRNA length of 26 to 33 bp and a minimum cluster length of 5000 bp. Genes falling within the detected clusters were retrieved according to Bt3.1 NCBI annotation, […]

[…] found different expression patterns in germline cells, different melanoma types and healthy skin.Prior to developing our own piRNA clustering pipeline we tested two already publicly available tools, proTRAC [] and piClust []. We excluded piClust, because of the restriction to selected genomes, file size and the limited number of multiple mapping sites per read. Using our dataset proTRAC resulted […]