Output File Documentation

Feature File

[Column 1] matchType - refName + maxMismatch + strand, e.g., "human_miRNA.mis_0+"

[Column 2] matchID - only consider the best mapped matchID for each unique read

[Column 3] readNum - sum of readNum mapped to the best matchID

Profile File

[Column 1] matchType - refName + maxMismatch + strand, e.g., "human_miRNA.mis_0+"

[Column 2] readID - ID-readNum

[Column 3] readSeq - original read sequence (even if orientation is -)

[Column 4] matchID - entry ID of the best match for each unique read

(for RNA, it is the first forward best match, if there’s one)

[Column 5] offset - readStart + mismatch for the best mapped matchID

(coordinate + CIGAR string, e.g., "6,22:C>A,23:G>T")

[Column 6] matchNum - number for how many multiple matchIDs for each unique read

[Column 7] multiMatch - other matches (NOT including the best match)

(format: "matchID_i|strand_i|offset_i|.|…")