The format required for providing quantification results by the user should be a tab-separated matrix in which long read-defined transcripts will be the rows and samples/replicates will be columns.
- Header: First field must be
IDand the rest of the column names should be the sample/replicates labels. - ID column: Transcripts should have the same IDs as ones provided in GTF.
- Quantification values reported: Any metric is acceptable as long as they correlate with RNA concentration. This can be evaluated using known concentration of SIRVs.
NAvalues are allowed.
Gene expression will be calculated summing up the expression values of all the transcripts coming from the same locus.
ID sample1 sample2 sample3 sample4
PB.1.1 49.98 49.22 75.64 60.10
PB.10.1 39.67 42.66 4.74 4.68
PB.10.2 33.08 29.32 5.37 8.42
PB.10.3 0.38 0.77 1.54 1.03
PB.100.1 37.57 36.33 18.97 22.78
PB.1000.1 184.49 157.44 44.97 71.41
PB.1000.3 1.46 1.46 0.43 0.83
PB.1000.4 7.21 7.50 4.95 1.65
PB.1000.5 13.38 14.55 0.33 3.32
PB.1000.6 2.53 6.68 8.29 11.26
PB.1000.7 3.44 2.14 2.31 1.99
PB.1000.9 48.80 66.51 31.94 30.00
PB.1001.1 1044.55 1134.42 382.44 314.14
PB.1002.1 342.16 348.46 148.90 240.40
PB.1002.2 882.45 926.07 575.31 715.36
PB.1003.1 19.04 21.93 30.88 43.33
PB.1003.2 22.54 15.69 76.57 79.59