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miRDeep2 changelog

Version 2.0.1.2

  • fixed uninitialized value errors/warnings

  • rephrased available species message

  • fixed Travis CI (still used to use ~/.bash_profile rather than ~/.bashrc)

Version 2.0.1.1

  • improved detection of installation directory & Rfam indices

  • instead of fractions, percantages are used in read statistics

  • several minor improvemnts to the MRD output format

  • negative repeat count warnings have been removed

  • HTML output does not contain (now dead) links to (old) Rajewsky lab webpage anymore

  • install.pl now modifies ~/.bashrc rather than ~/.bash_profile

  • miRDeep2.pl now handles changed RNAfold output

Version 2.0.1.0

  • fixed bug resulting in negative repeat count due to too small -l value

  • braces in regex were escaped [deprecated by upstream]

  • miRDeep2 was licensed under GPL v3

  • the documentation was improved and converted to Markdown

  • minor improvements and code cleanup

  • the tutorial is now run via Travis CI on Linux & Mac to test the build

  • Sean Eddys squid libray was removed from the repository

Version 2.0.0.8

  • The install.pl script has been updated to download automatically the latest PDF::API2 version and the latest bowtie1 version.

  • Source code has been cleaned up and pathes have been adapted. So when using this version please do a new installation of miRDeep2 and do not just copy scripts over old version. Otherwise your installation will likely be broken.

  • RNAfold and randfold now compile again on MacOSX 10.10.5 due to adaptation of the fold.c source file in these packages.

  • minor issues removed

  • code is cleaned up and installation directories are also organzied more reasonable

  • Sean Eddys squid libray is included in the package already since the download server is sometimes not to be working

Version 2.0.0.6

  • corrected bed file coordinates, off by one error fixed

  • the zebrafish switch works now in the species specification

  • novel detected miRNA sequences by the miRDeep2 module are now stored in separate files

  • in the mapper module all tmp files are deleted now when the specific option is given

  • install.pl script has been updated in regards of program download links

  • additional file checks were included for the mapper module when using options a, b, c, or e

  • novel detected miRNA sequences and bed coordinates are output automatically now

Version 2.0.0.5

  • The quantifier.pl has a new switch -U that causes the usage of only uniquely mapping reads to reference precursors.

  • The mapper.pl reports now the number and percentage of mapped and unmapped reads from the collapsed reads file to a reference genome.

  • miRDeep2 now aborts when no precursors were excised.

  • A BED file of all miRDeep2 detected precursors is created in the end.

  • An additional check of the ARF file ids and genome file ids was added to make sure that ids in both files really match.

  • An additional check for the presence of the Rfam indices was added.

  • A bug was fixed that occurred when the miRDNA IDs were too long.

  • The HTML file in the end does not abort anymore when the Rfam index is missing.

Version 2.0.0.4

  • The quantifier.pl now calculates correctly the remaining read counts.

  • Reads that map to more than one precursor are now added in a weighed way to each precursor. The normalization of read counts in the quantifier.pl has changed a bit. Each miRNA read count is now divided by the total number of sequenced miRNA read counts and then multiplied by 10E9.

  • The --strata option is added to mapping of reads to the miRBase precursors in the quantifier module.

  • The miRDeep2 html output has been updated so that for known miRNAs the field mature miRBase miRNA now contains the miRNA that matches the predicted mature sequence or in case that the predicted star sequence matches a known miRNA this is then shown instead.

  • The install.pl script can also use curl if wget is not available on the machine. This is useful for MACOSX users.

  • The mapper.pl now also determines the number of cores on Mac machines correctly.

  • A bug has been fixed in the prepare_signature.pl file. It crashed when no known_mature_mirna file was supplied.

  • RNAfold2 can be used as well now if already installed. Otherwise version 1.8.4 of the Vienna package is downloaded when running the install.pl script.