2022-06-15
  • Version 1.3.0
  • meRanCall:
    Implemented a C-cutoff filter. Removes reads from poor conversion in the sense that if a read has more than C_cutoff Cs it will not be considered in m5C calling.

    Implement signal to noise ratio filter. Only consider sites that have a SNR higher than signalToNoise

    Implement a minimum C filter. Only consider sites that hav a minimum of minC Cs.

    Implemented gene level CR. meRanCall can now calculate the CR for each individual gene from a provided GTF file. This CR is than used in the statistical tests for the candidate sites in a corresponding gene.

    Implemented conflict solving for overlapping mates of a read pair. Only one base call, namely the one of the mate with the better quality score, is considered.
  • meRanGs, meRanGh, meRanT:
    updated third party programs: STAR, HiSat2, bowtie2
  • provide a conda env YML file for meRanTK
  • added support for the current RefSeq mRNA fasta files from NCBI the mkRefSeq2GeneMap.pl utility.
  • minor fixes
2019-01-29
  • Version 1.2.1b
  • meRanGh, meRanGs, meRanT:
    bugfix for correctly processing gzipped fastq files.
    reported by Sangrea Shim
  • meRanGh, meRanGs:
    bugfix for dovetailing reads which were filtered out even if -dt was set. Note: -dt option needs STAR version 2.6.1d
    reported by Jianheng Liu mail2.sysu.edu.cn>
  • meRanGs:
    Added support for STAR_2.6.1d
  • meRanCall:
    bugfix for situations where only reverse reads are provided.
    reported by Andrew Janowczyk unil.ch>
2018-05-25
  • Version 1.2.1a
  • meRanGh:
    bugfix for situations where only reverse reads are provided. reported by Andrew Janowczyk unil.ch>
2018-05-25
  • Version 1.2.1
  • meRanGs, meRanGh:
    circumvent file locking issues seen on some systems during concurrent writing.
  • meRanCall:
    added Fisher exact Test as statistical methylation state test
  • meRanAnnotate:
    fixed dereference error
2016-09-29
  • Version 1.2.0
  • NEW tool meRanGh
    Implemented a new RNA-BSseq aligning tool called meRanGh. The tool is using the alignment engine from HiSat2. Is is comparable in speed to meRanGs but has a substatially lower memory requirement.
  • Deprecating meRanGt:
    ! meRanGt is now deprecated ! It will not be developed any further.
  • meRanGs:
    Added support for STAR_2.5.2b fixed alignment score bug (AS:i:0 was set to -1_000_000)
2016-07-07
  • Version 1.1.2
  • mkRefSeq2GeneMap.pl: fixed a bug (last sequence in fasta was ignored) reported by Jun Li (jun.li04adelaide.edu.au)
2016-06-23
  • Version 1.1.2
  • small fixes
  • meRanT: check for empty gene name when trying to add gene names in SAM output
  • meRanT: check bowtie2 version and require 2.2.9 (or greater)
  • meRanT: use multithreaded index building option from bowtie 2.2.9
  • meRanGt: require tophat2 version 2.1.1 (or greater)
  • meRanGs: added support for STAR_2.5.2a
2016-02-29
  • Version 1.1.1b
  • small fixes
2015-01-12
  • Version 1.1.1a
  • meRanGt includes a patched version of tophat2 to support large bowtie2 indexes (suggested by Sven E. Templer)
  • updated included bowtie2 to version 2.2.6
  • small fixes
2016-01-11
  • Version 1.1.1
  • Added support for STAR version STAR_2.5.0c
  • Added '-star_limitGenomeGenerateRAM' option to limit memory usage during index generation in mkbsidx mode (suggested by Sven E. Templer)
2015-08-17
  • Version 1.1.0
  • Added support for STAR version STAR_2.4.2a
  • merged "MP" version code into the main version it seems to be stable
  • Added meRanCompare (experiment comparison)
  • Added meRanAnnotate (m5C annotation tool)
  • Added Aza-IP support for meRanCall and meRanCompare
  • Improved BH FDR methods
  • Added Fisher's exact test to meRanCall to compare candidate with baseline sequencing error (used if conversion rate is unknown)
  • Added "-region" option to meRanCall to call only m5Cs in regions specified in a given BED file
  • Added "-excludeSeqID" option to meRanCall to exclude a given sequence/chromsome from m5C calling
  • docs updates
  • many small improvements and bug fixes
2015-04-07 Added support for new STAR version STAR_2.4.0k
2015-03-31 Added speed improved versions for meRanGs and meRanGt: meRanGsMP cuts the running time of meRanGs down to ~55% meRanGtMP cuts the running time of meRanGt down to ~85% The two versions now make (better) use of multiprocessing They are still not fully tested, so we consider them beta. However, our tests did all run sucessfully so far. The "MP" versions will be merged into the main versions soon.
2015-02-17 First publicly available version of meRanTK is online              
(see Download)