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RELEASE NOTES FOR SeqMonk v1.42.1
This release was an opportunity for a general cleanup of a lot of cosmetic
issues which had been building up, as well as addressing a number of bugs.
Things which we fixed were:
Fixed the text alignment on a lot of plot axes to be more pretty
Fixed a data scaling bug on the QQ plot which sometimes missed out the
Fixed a crash in LIMMA when data contained NA values
Fixed a cancellation bug in the HiC heatmap
Fixed a null pointer bug in the proportion of library bug
Added an option to save the data from the quantitation trend plot
Added whitespace support to generic text import
We now record the import options used when importing data
Handle platforms where we can't automatically open a web browser better
Fixed a bug where the read position probe generator only did a single chromosome
Improved the layout of the quantitation trend heatmap
Fixed a bug with NA or infinite values in the quantitation trend plot
RELEASE NOTES FOR SeqMonk v1.42.0
This release has a fix for a potentially nasty data import bug introduced in
v1.40.1 and adds some new visualisation features.
Important Data Import Bug
We are indebted to John Chuang for spotting a data import bug which was
introduced in v1.40.1 and which could corrupt data imported from sorted
BAM files containing duplicated sequences. We'll do a full write up
elsewhere but the details of the bug can be seen in:
In short, if you have imported a sorted BAM file using SeqMonk v1.40.1 or
v1.41.0 then you may have had some duplicate reads silently discarded. The
issue could also theoretically affect sorted files, but the number of
sequences affected would be extremely low and is unlikely to materially
affect any datasets.
Projects which had data imported in an earlier version of seqmonk, and the
project was opened and saved in the affected versions are not affected.
The bug is in the import step.
If you imported sorted files into an affected version of the program then
we recommend that you create a new project and re-import the BAM files
using seqmonk v1.42.0 (or later).
Other changes in this release:
Added a size factor normalisation quantitation
Fixed a data update bug when creating custom genomes
Added a new Quantitation Trend Heatmap plot, and optimised the old
Quantitation Trend Plot code
Worked around an EdgeR installation bug which caused the EdgeR
filter to break.
Fixed a problem with the linux themeing on Ubuntu 18.04
This release adds some new functionality, but also tidies up a lot of existing
features, making them work more smoothly.
Added a QQ plot
Improved the options and multiple testing correction in the logistic
Fixed a slowness issue when working with hundreds of samples.
Added a mechanism to allow projects to update to newer versions of
core annotations in the same assembly.
Added a fix for the RNA-Seq QC plot when there isn't a rRNA track in
Modified the DESeq filter to allow multiple group comparisons by using
the Likelihood ratio test.
Report the parameters estimated by the RNA-Seq pipeline.
This is a bugfix release of seqmonk which adds some optimisations to the
background data model and fixes a number of bugs.
Changed the internal data model to store positions and counts separately
to make the storage of heavily duplicated data much more efficient
Added a LIMMA statistical filter
Modified the GTF parser to better deal with the structure of Ensembl
Changed all of the launchers so you can pass a file name to open. Allows
file extensions to be associated with seqmonk so you can open projects
by double clicking on them.
Improve the merging of transcripts in the RNA-Seq pipeline to use
gene ids where they are present in the annotation so we don't get
spurious merging of overlapping transcripts on the same strand which
are annotated as belonging to different genes.
Updated the genome processing scripts so that gene_ids are added to
Fixed a crash in the aligned probes plot when no data stores are visible
Fixed a display bug for the list of features in the feature filter and
quantitation trend plot.
Fixed an inefficient packing algorithm when the number of reads was too
great to be displayed within the available height of the chromosome view.
RELEASE NOTES FOR SeqMonk v1.40.0
This release does some major reorganisation of the filtering menu as well as
adding new functionality. Major changes are:
Completely restructured the statistics filter menus so that they are
now arranged by the type of data they apply to.
Added an option to detect and remove duplication in the RNA-Seq
Added a new variant of the EdgeR filter which can work on for/rev
ratio data such as methylation data.
Added an option to change the startup memory settings from the usual
Added an R debug mode to make it easier to track down problems with R
Fixed a bug in the variation plot for data containing NaN values
Fixed a regression which meant some functionality didn't work on systems
running java 1.6
Added an option to create data groups or replicate sets from pre-prepared
lists of data store names.
Added a global correction to the aligned probes plot to make the plots
more directly comparable.
Fixed a bug in the exporting of images from the aligned probes plot.
Collated error messages to help interpreting large numbers of errors.
Added a strand bias plot
This release is a mix of new features and bug and usability fixes for existing
features. Major changes are:
Added the ability to have multiple annotation versions for the same genome
assembly release. We needed a way to update the annotations used for some of
the major eukaryotic genomes, when the sequence level assembly hadn't actually
changed. All genomes can now have multiple versions distinguished by the Ensembl
release number from which they came. The genome selection interface now shows
the different annotation versions for the same genome assembly grouped together.
Added a parser for the BEDPE file format
Added a better filtering for absolute change to the binomial, chi-square and
logistic regression filters.
The hierarchical cluster plot now allows for the highlighting of replicate sets
at the top.
The gene set filter now provides the option to use the Kolmogorov-Smirnov test
as well as the t-test when finding changing gene sets
Altered the feature filter to allow it to simultaneously use multiple feature tracks
Improved the scaling of the aligned probes plot so that the absolute numbers reported
are more meaningful
Added a scale bar to the aligned probes plot
Fixed a crash in the PCA plot when no data remained after removing null values
Fixed a crash when saving results from the correlation matrix
Fixed a bug which allowed replicate sets to be added to other replicate sets
when auto-creating sets in the data store tree
This is a bugfix release which mainly addresses a bug in the most recent
jave release on OSX. Specific changes in this release are:
Fixed a hang bug specifically triggered in java v1.8_131 when creating
any report. The bug doesn't affect other platforms, or previous versions
of the JRE.
Fixed a problem with the auto-setup of the perplexity setting in the Tsne
plot which affected projects with fewer than 7 samnples.
Fixed a bug which caused the intensity gene set plot to not clean up
temporary probe lists when the list of hits was sorted.
This is a bugfix release which addresses some issues found in the previous
We fixed a performance bug when creating custom genomes from fasta or gff
files with very large numbers of sequences in them. This would have affected
people building custom genomes from very fragmented sets of contigs.
We added a scale bar to the HiC heatmap
We changed the TSNE code to use Rtnse instead of tsne to work round a bug and
to improve performance
We added some more debugging output to the launch script to make it easier to
debug launching problems
We fixed a bug in the SplicingEfficiency pipeline affecting genomes with
non-Ensembl naming schemes
We fixed a bug in PCA plotting when showing labels in plots with overlapping
This release adds some new plotting options for data store similarity and greatly improves the workflow for the analysis of splicing as well as adding some more general bug fixes and improvements.
Major changes are:
Added a TSNE plot for clustering data stores
Added colouring to the correlation matrix
Added a logistic regression splicing statistical filter
Greatly improved the efficiency of the exactly overlap quantitation
Added strand information to probe reports
Fixed a bug in the launcher for UTF8 locales
Fixed a bug in the normalisation of paired end RNA-Seq data
Fixed a crash in bioconductor installation
RELEASE NOTES FOR SeqMonk v1.37.1
This release is a minor bugfix release. Updating to this release is only
necessary for people directly affected by one of the bugs below:
- Fixed a bug in the reporting of R errors where the full R trace wasn't
attached to the crash report making it difficult to identify the cause
of R problems.
- Fixed a bug in the generation of custom genomes where feature names
containing a forward slash in their names would cause a failure of the
feature caching system.
- Fixed an out of date warning in the RNA-Seq pipeline which hadn't been
updated to the new option names in the BAM import dialog.