diff --git a/HELP.md b/HELP.md index efd3b4f..e2b11c1 100644 --- a/HELP.md +++ b/HELP.md @@ -88,6 +88,7 @@ A2A6A1 | O88898,P54763,Q3UHC0 | G5E870 | Q6A037 | + | Example "Allowed": @@ -97,6 +98,7 @@ comp1000309_c0_seq1|slc15a3|Q8IY34,O75618 | comp1000318_c0_seq1| | | comp1000627_c0_seq1|slc6a15|sp|Q9XS59|S6A15_BOVIN | comp1000899_c0_seq1| |gb|CX212397.1,dbj|DB530926.2,gi|154363325| + | #### miRNA File (-im) @@ -114,6 +116,7 @@ hsa-miR-93b-5p| miR-36f| mmu-miR-29d-3p| miR-29c| + | Example "Allowed": The example is a part of an original output of the MIRPIPE pipeline (Kuenne et al., 2014), which the LimiTT parameters are adjusted to. @@ -124,6 +127,7 @@ miR-93b|52 |1.00|170|CAAGTGCTGTTCGTGCAGGTAG|33 | miR-36f|211 |0.00|171|ATTGAGCTATCTGTGTAG |211 | miR-29d|141233|0.02|172|TAGCACCATATGAAATCAGTGT|133582| miR-29c|55690 |1.00|172|TAGCACCATTTGAAATCGGTTA|44200 | + |||||| #### Ranking File (-ir) @@ -143,6 +147,7 @@ Q3UHC0|0.931454837| O88898|0.240325584| G5E870|0.47554716 | Q6A037|0.495874819| + | | ### Output @@ -160,13 +165,13 @@ The order of the DBs for the binary string can be found in the first row. Example: -|Database order: TarBase, miRTarBase, miRecords, starBase| -|------|-----|-------|------|-------|------|-------------| -| |miR-9|miR-15a|miR-17|miR-19b|miR-24| miR-26a | -|A0AVK6| 0001| | | | 0110| | -|A2A6A1| | | | 1110| | | -|A2AAY5| | | 1110| | | 1001 | -|A2AHG0| |0001 | 0101| | | | +Database order: TarBase, miRTarBase, miRecords, starBase||||||| +------|-----|-------|------|-------|------|-------------| + |miR-9|miR-15a|miR-17|miR-19b|miR-24| miR-26a | +A0AVK6| 0001| | | | 0110| | +A2A6A1| | | | 1110| | | +A2AAY5| | | 1110| | | 1001 | +A2AHG0| |0001 | 0101| | | | #### MTI Info