Criteria for including reads.
Criteria for internal priming.
We follow the standard BED specification with 0-based coordinates. Additionally, we appended extra column(s). For more information click here.
The columns represent:
first - chromosome name
second and third - start and end positions of the poly(A) site cluster, respectively
fourth - unique cluster ID, composed of the chromosome name, the representative poly(A) site of the cluster and the strand. Note that this ID format is inspired by UCSC's position format, which uses 1-based coordinates instead of the 0-based bed coordinates used in the second and third columns. Thus, to convert the position of the representative site to bed coordinates, subtract 1.
fifth - expression (tags per million, tpm) in this sample
sixth - strand on which the cluster is encoded
seventh - percentage of samples that support the particular cluster
eighth - number of different 3' end sequencing protocols that support the particular cluster
ninth - average expression (tags per million, tpm) across all samples
tenth - two letter code for the cluster annotation (in order of decreasing priority: TE, terminal exon; EX, exonic; IN, intronic; DS, 1,000 nt downstream of an annotated terminal exon; AE, anti-sense to an exon; AI, anti-sense to an intron; AU, 1,000 nt upstream in anti-sense direction of a transcription start site; IG, intergenic)
eleventh - information about the poly(A) signal(s) that are present upstream of the poly(A) site, including the motif, the location with respect to the cleavage site and the genomic coordinate