MIR
From Icbwiki
Usage
MIR provide miRNA predicted targeting site analysis at 3'UTR. It can analyze the RNA-seq reads with putative polyA-tail and see if there is any miRNA targeting site changes from a 3'UTR length changes with the longest form of 3'-UTR. We analyze 711 miRNAs' targeting site in mirA. The miRNA targeting site finding is strand-specific.
There are two format of output for MIR. One is format T: the miRNA targeting site is in table. So the miRNA table would be 711 columns. This format is convenient for statistical software to read-in. Another is format R: the miRNA targeting site information is in the style of "miRNA#count;". This format is easier for user to directly read.
$ cd TBAG/
For format T, the command is:
$ ./mir T AceView/ human_miRbase.txt miRlist sample/pol_output mir_output
For format R, the command is:
$ ./mir R AceView/ human_miRbase.txt miRlist sample/pol_output mir_output
Output Format
The format of MIR output is following. In the 7th column, "F" stands for the full length 3'UTR of the according transcript, "1P" stands for the truncated 3'UTR by the first putative polyA tail site of the according transcript and "1D" stands for the miRNA targeting difference between "F" and "P". If there are multiple putative sites in the 3'UTR of certain transcript, there could be "2P", "2D", "3P", "3D"...
Format T chr strand gene_name transcriptID putative_polyA 3'UTR_locus 3'UTR_type 3'UTR_exon_num polyA_tail_base_num read_counts hsa-let-7a hsa-let-7a* hsa-let-7b ... chr6 + CDKN1A CDKN1A.kApr07 36763083 36761553-36763094 F 3 0 0 1 0 0 ... chr6 + CDKN1A CDKN1A.kApr07 36763083 36761553-36763094 1D 3 5, 1 0 0 0 ... chr6 + CDKN1A CDKN1A.kApr07 36763083 36761553-36763094 1P 3 5, 1 1 0 0 ... Format R chr strand gene_name transcriptID putative_polyA 3'UTR_locus 3'UTR_type 3'UTR_exon_num polyA_tail_base_num read_counts miRNA#counts; chr19 + SNRP70 SNRP70.eApr07 54303543 54303510-54303681 F 3 0 0 hsa-miR-7-1*#1;hsa-miR-589*#1;hsa-miR-139-3p#1;hsa-miR-523#1;hsa-miR-7-2*#1;hsa-miR-423-5p#2;hsa-miR-362-3p#1;hsa-miR-611#1;hsa-miR-612#1;hsa-miR-590-3p#1;hsa-miR-614#1;hsa-miR-362-5p#1;hsa-miR-768-5p#1;hsa-miR-95#1;hsa-miR-296-3p#1;hsa-miR-873#1;hsa-miR-421#1;hsa-miR-922#1;hsa-miR-339-3p#1;hsa-miR-432#1;hsa-miR-936#1;hsa-miR-525-3p#1;hsa-miR-92a-1*#1;hsa-miR-524-3p#1;hsa-miR-672#1;hsa-miR-885-3p#1;hsa-miR-214#1; chr19 + SNRP70 SNRP70.eApr07 54303543 54303510-54303681 1D 3 5, 1 hsa-miR-7-1*#1;hsa-miR-589*#1;hsa-miR-139-3p#1;hsa-miR-523#1;hsa-miR-7-2*#1;hsa-miR-423-5p#2;hsa-miR-362-3p#1;hsa-miR-611#1;hsa-miR-612#1;hsa-miR-590-3p#1;hsa-miR-614#1;hsa-miR-362-5p#1;hsa-miR-768-5p#1;hsa-miR-95#1;hsa-miR-296-3p#1;hsa-miR-873#1;hsa-miR-421#1;hsa-miR-339-3p#1;hsa-miR-432#1;hsa-miR-525-3p#1;hsa-miR-92a-1*#1;hsa-miR-524-3p#1;hsa-miR-672#1;hsa-miR-885-3p#1; chr19 + SNRP70 SNRP70.eApr07 54303543 54303510-54303681 1P 3 5, 1 hsa-miR-214#1;hsa-miR-922#1;hsa-miR-936#1; chr6 + PACSIN1 PACSIN1.bApr07 34610762 34608283-34611307;34611378-34612016; F 10-11 0 0 hsa-miR-323-3p#2; chr6 + PACSIN1 PACSIN1.bApr07 34610762 34608283-34611307;34611378-34612016; 1D 10-10 5, 1 chr6 + PACSIN1 PACSIN1.bApr07 34610762 34608283-34611307;34611378-34612016; 1P 10-10 5, 1 hsa-miR-323-3p#2;
Each line contains:
| Column | Field | Discription |
|---|---|---|
| 1 | chr | chromosome number |
| 2 | strand | The strand of the putative polyA-tail |
| 3 | gene_name | The gene name of the reads with putative polyA-tail |
| 4 | transcriptID | The transcript ID of the reads with putative polyA-tail |
| 5 | putative_pola_site | The 1-base in front of start position of the putative polyA-tail |
| 6 | 3'UTR_locus | The full version of 3'UTR "start position-stop position"; 3'UTR expand multiple exons will be separated by ";" |
| 7 | 3'UTR_type | Indicate different 3'UTR form data: "F":the full length 3'UTR of the according transcript;
"1P": the truncated 3'UTR by the first putative polyA tail site of the according transcript; "1D": the miRNA targeting difference between "F" and "P". Multiple putative sites in the 3'UTR of certain transcript could be present as "2P", "2D", "3P", "3D"... |
| 8 | 3'UTR_exon_num | The exon number covered by the 3'UTR |
| 9 | polyA_tail_base_num | The putative polyA-tail base number |
| 10 | read_counts | The read counts at the 1-base in front of start position of the putative polyA-tail |
| 11 | miRNA targeting information | Format T: 711 column of different miRNAs' targeting information using the number of targeting site within the 3'UTR for each miRNA;
Format R: 1 column for miRNA and its targeting site number in for the 3'UTR. Multiple miRNA are separated by ";" |
