README.md

February 16, 2017 · View on GitHub

Authors

Ernest Turro wrote all the code in this package except

  • hitsio library: Jürgen Jänes
  • readmmseq R function: Angela Goncalves and Ernest Turro
  • ensembl_gtf_to_gff.pl: user 'genec' on seqanswers.com
  • sokal.cc/hh: Graeme Ambler
  • fasta.c/h: Bio5495/BME537 Computational Molecular Biology, Michigan State University

Changelog

  • 2017-02-16: MMSEQ 1.0.10 released, bam2hits works with kallisto-generated bams
  • 2016-06-02: MMSEQ 1.0.9 released, various fixes and improvements; in particular, fixed bug in the MCMC update for eta in mmdiff which could result in an exception (this did not affect standard differential expression)
  • 2014-01-23: MMSEQ 1.0.8a released, new linux binaries (old ones linked to a dodgy version of boost)
  • 2014-01-09: MMSEQ 1.0.8 released, mmcollapse bugfix (incorrect SDs sometimes output previously)
  • 2013-11-11: MMSEQ 1.0.7 released, performance improvements to mmcollapse; added code to generate strain-specific transcriptome and genome FASTAs
  • 2013-09-20: MMSEQ 1.0.6 released, added percentiles output to mmseq (e.g. to obtain credibility intervals); various minor improvements
  • 2013-06-16: MMSEQ 1.0.5 released, fixed bug in mmdiff beta update; added polyclass() R function for polytomous model classification
  • 2013-06-11: MMSEQ 1.0.4 released, fixed bugs in mmdiff apparent when M.n_cols > 1
  • 2013-06-09: MMSEQ 1.0.3 released, fixed beta update (covariates common to all models can now be taken into account); added -de convenience option for mmdiff; also fixed harmless bug that could strip first character of sample names in mmdiff output header
  • 2013-04-26: MMSEQ 1.0.2 released, better prior for eta in mmdiff (Inverse-Gamma)
  • 2013-04-08: MMSEQ 1.0.1 released, including new binaries mmcollapse and mmdiff (publication forthcoming)
  • 2012-12-06: MMSEQ 1.0.0 beta released (more mmseq output: estimates for features even if they have no reads, output posterior standard deviations, whether or not features have been observed, etc. Improved normalisation procedure in readmmseq.R and mmdiff (using only features with unique hits in a minimum proportion of samples). Beta versions of mmcollapse and mmdiff programs. Inclusion of t2g_hits program.)
  • 2012-05-28: MMSEQ 0.11.2 released (output mean posterior isoform/gene expression proportions)
  • 2012-04-19: MMSEQ 0.11.1 released (output true sequence lengths in addition to effective transcript lengths)
  • 2012-04-16: MMSEQ 0.11.0 released (bam2hits updates: print nice ASCII insert size histogram to check it's roughly normal; -i option now uses expected_isize and sd_of_isizes (instead of deviation_thres); unless adjusted lengths are provided or calculated with mseq (options -c and -u), transcript lengths are adjusted using the insert size distribution - the prior fragment distribution given the transcript is assumed to be uniform up to the transcript length within the main support of the insert size distribution; proper repetitive transcript filter applied before simplified isize deviation filter; deal gracefully with truncated hits files)
  • 2012-03-26: MMSEQ 0.10.0 released (new hitsio library by Jürgen Jänes results in ~7x reduction in hits file sizes - inspection of compressed binary hits files and conversion to plain text can be done with the hitstools utility; fixed default regex to work with new (>v64) Ensembl fasta entry naming convention; more information in *.mmseq tables; output gzipped MCMC traces; improved readmmseq.R script)
  • 2011-12-16: MMSEQ 0.9.18 released (the *.mmseq files now contain all the transcripts or genes, regardless of whether they have counts; improved R script to read in the output (readmmseq.R); fixed potential integer overflow if gibbs_iter set too high; default gibbs_iter doubled to 2142^{14}, though there can be a noticeable reduction in autocorrelation up to 2172^{17} iterations)
  • 2011-11-07: MMSEQ 0.9.17 released (misc. improvements and small bugfix in bam2hits code for identifying read mates)
  • 2011-10-21: MMSEQ 0.9.16 released (output mean(log) rather than log(mean) of expression parameter; output expression-weighted sum of transcript lengths in gene files; misc other changes)
  • 2011-10-17: MMSEQ 0.9.15 released (automatically set insert size deviation filter parameters; remove read length - 1 from effective transcript lengths; added extract_transcripts program to produce sequences from genome FASTA and Ensembl-like GTF files)
  • 2011-09-22: MMSEQ 0.9.14 released (workaround for bug in Mac gcc that causes omp_get_max_threads() to incorrectly return 1 if called from a parallel region - estimates obtained on Mac with previous versions of mmseq are probably invalid)
  • 2011-09-20: MMSEQ 0.9.13 released (changed default prior on mu to Gamma(0.1,0.1), which appears to reduce upwards bias for lowly expressed transcripts; all mmseq parameters can now be controlled from the command line; include mmseq2counts.R for DE analysis)
  • 2011-08-15: MMSEQ 0.9.12 released (bug fix for potential seg fault)
  • 2011-06-12: MMSEQ now available on Fedora 14/15 and EPEL 5/6 (yum install mmseq). Many thanks to Adam Huffman.
  • 2011-06-07: new version of polyHap2 released with support for random assignment of alleles to haplotypes
  • 2011-05-27: MMSEQ 0.9.11 released (fixed bug in insert size deviation filter in bam2hits)
  • 2011-05-04: MMSEQ 0.9.10c released (ensured haploref.rb works properly with custom regular expressions - same behaviour as testregexp.rb and bam2hits; fixed bug in identical transcript/gene amalgamation code. Prior to 0.9.10, incorrect values outputted in *.amalgamated.mmseq and *.gene.mmseq files if one of the transcripts had zero hits and no values outputted in *.gene.mmseq for genes with log Gibbs mean < 0)
  • 2011-03-18: MMSEQ 0.9.9 released (better integration with 'mseq'; deal gracefully with Ns in counts file; harmless buffer overflow bugfix in bam2hits)
  • 2011-02-10: MMSEQ paper published in Genome Biology
  • 2010-10-19: MMSEQ 0.9.8 released