License

Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.

Requirement

This program is developed in Linux environment.
It requires bedtools, gtfToGenePred, and Python with numpy and rpy2 package for running.

Program

Name Description Download
GETUTR (source code) 2.0.0 Download

Essential Reference Files

Essential files for GETUTR

Name Description Download
refFlat reference human genome (hg19) Download

Sample Files

We provide sample files: two input files and their corresponding output files.
HeLa_Puc19_all.bam contains RNA-seq reads (NCBI GEO accession number: GSM1269348 and GSM1269349). It sequenced from HeLa cells are mapped to the reference genome (hg19).

Name Description Download
HeLa_Puc19_all.bam Mapped reads from HeLa cells Download
HeLa_Puc19_all.PAVA.smoothed.bed smoothed 3' UTR from HeLa_Puc19_all.bam Download
HeLa_Puc19_all.PAVA.PCS List of PCSs at HeLa_Puc19_all.PAVA.smoothed.bed Download
HeLa_Puc19_chr22.bam chr22 part of HeLa_Puc19_all.bam Download
HeLa_Puc19_chr22.PAVA.smoothed.bed smoothed 3' UTR from HeLa_Puc19_chr22.bam Download
HeLa_Puc19_chr22.PAVA.PCS List of PCSs at HeLa_Puc19_chr22.PAVA.smoothed.bed Download

HeLa_Puc19_all.bam

...
WICMT-SOLEXA2_0010_61BJ1AAXX:7:20:13345:19180#0/1;1     16      chr1    14576   255     35M     *       0       0       *       *       XA:i:0  MD:Z:35 NM:i:0  RG:Z:HeLa_Puc19_1_exj
WICMT-SOLEXA2_0010_61BJ1AAXX:7:14:5424:2434#0/1;1       16      chr1    14578   255     35M     *       0       0       *       *       XA:i:0  MD:Z:0A0G0T1C30 NM:i:4  RG:Z:HeLa_Puc19_1_exj
WICMT-SOLEXA2_100602_6226EAAXX:7:42:5292:11083#0/1;1    16      chr1    14578   255     35M     *       0       0       *       *       XA:i:0  MD:Z:0A0G0T0G0C0T1G27   NM:i:7  RG:Z:HeLa_Puc19_2_exj
WICMT-SOLEXA2_0010_61BJ1AAXX:7:68:7498:17668#0/1;1      16      chr1    14581   255     35M     *       0       0       *       *       XA:i:0  MD:Z:35 NM:i:0  RG:Z:HeLa_Puc19_1_exj
...

HeLa_Puc19_all.PAVA.smoothed.bed

track name="GETUTR_bed" type=bedDetail description="3' UTR of NM_001143984 by GETUTR"
chr11	47593115	47593272	1.0	+
chr11	47593272	47593282	0.950050821127	+
chr11	47593282	47593293	0.861667232993	+
chr11	47593293	47593303	0.763876049381	+
chr11	47593303	47593314	0.664680181248	+
...

HeLa_Puc19_all.PAVA.PCS

track name="GETUTR_PCS" description="PCS of NM_001143984 by GETUTR"
chr11	+	47593303	0.944507539913
chr11	+	47593627	0.0175641041048
chr11	+	47595024	0.030923706495
chr11	+	47595743	0.00528573989001
chr11	+	47597672	0.00171890959703
...