Please cite: An, J., Lai, J., Lehman, M.L. and Nelson, C.C. (2013) miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data. Nucleic Acids Res, 41, 727-737.
We will create index for you if you tell us your interested species (j.anATqut.edu.au).
download command line version "MDS_command_line_Vxx.zip" clicking "Browse All Files"
please find miRPlant in sourceforge for plant miRNA prediction.
Feature
- v37 for solving new attribute nM used in STAR aligner
- java source code "MD.zip" can be found clicking "Browse All Files" on the right corner of this windows. Netbeans IDE was used
- speeded up in v36
- v35 fixed a bug that gives "error:java.lang.IllegalArgumentException: Comparison method violates its general contract!" when score is very big
- bug fixed. in v32, the read count was incorrect in xxxx.known_miR.result file, when the inputted bam file was generated in third party aligner such as BWA etc.
- bug fixed. In v31, null exception appeared when clicking "save image" in the popup window in MacOS.
- the images generated with "save image" could not be accepted by corelDraw, it is fixed in miRDeep_star_v31. [in source code, adding "g.setFontRendering(VectorGraphics2D.FontRendering.VECTORS)"]
- miRDeep_star_v31 and MDS_command_line_v32 will produce a new file “xxx.known_miR.result” in the dat folder, which records expression level for all known miRNAs based on the file knownMiR.gff3. 22/12/2013
- in mirDeep_star_v31 and MDS_command_line_v32, the read sequence in bam file becomes constant plus strand genome sequence instead of read sequence
- build_bwt_index_v3.zip converts "Y", "R" and etc. in genome charators into "N" to avoid exception.
- MDS_command_line_v32.zip fixed the bug: integer parameters could not be inputted.
- miRDeep_star_v31 and MDS_command_line_v31 have removed DecimalFormat class which may cause Decimal seperator "." becomes "," and consequently, NumberFormat Exception happens.
- miRDeep_star_v3 and MDS_command_line_v3 have been fixed a bug in dealing with sam/bam file generated by third party alignment tools
- miRDeep_star_v2 and MD_command_line_v1 have been updated to account for the adapter located in the middle of reads for the case of "long" deep sequencing reads.
- miRDeep_star_v1 has a new function "save image" to save hairpin figure into "eps", "svg", or "pdf" file.
- build_bwt_idx_v2 fixed a bug in build_bwt_idx_v1 (it takes very long time to build index for genome sequence having large pieces of N)
- Integrated miRNA identification tool. NO third party tools (mapping tools, RNAfold) are needed
- MiRDeep* has a user-friendly graphic interface and accepts raw data in FastQ and SAM/BAM format
- Known and novel miRNA expression levels, as measured by the number of reads, are displayed in an interface which shows each RNAseq read relative to the pre-miRNA hairpin
- The human target genes of known and novel miRNAs are predicted using the TargetScan algorithm and the targets are ranked according to the confidence score
- miRDeep* can be used in other species, the BWT index files need to be built using built_bwt_index application
mirplant
please cite:
An J, Lai J, Sajjanhar A, Lehman ML, Nelson CC: miRPlant: an integrated tool for identification of plant miRNA from RNA sequencing data. BMC bioinformatics 2014, 15(1):275.
We will create index for you if you tell us your interested plants (j.anATqut.edu.au)....
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