Guillermo Barturen, Antonio Rueda, José L. Oliver and Michael Hackenberg
For questions and feedback, please contact to: MH - firstname.lastname@example.org, JLO - email@example.com, GB - firstname.lastname@example.org
News and releases
Solved exit silently when there is no methylation levels in a chromosome/scaffold (Thanks to Frank Wessely and Philippa Clare Griffin for reporting the bug)
Seq parameter explanation extended
Solved a bug during the binomial coefficient calculation on MethylExtractBSPvalue.pl (Thanks to Corey Wischmeyer for reporting the bug)
MAIN SCRIPT IMPROVEMENT
Gapped alignment handling improved
Checking parameters step removed
Solved a bug which affects to reads that go further than the reference assembly, this situation could appear when using seed alignment methods (Thanks to Dr. Huang for pointing out the bug and testing the developing version)
Solved a sequence output bug on CHH contexts
Included explanations to extract single chromosome reads and fasta sequences from multifasta files
MAIN SCRIPT IMPROVEMENT
Output subroutines rewritten (easier to understand and faster)
ADDITIONAL SCRIPTS IMPROVEMENT
Version removed from files names
SNVs Fisher strand bias threshold included
3' nucleotides filter included
Pair-End overlapping segments solution included
NEW FORMATS SUPPORTED
Multifasta support included
*.fas and *.fasta extensions are accepted as Fasta files
No context coverage warning included (probably due to a Qscore or FLAGs erroneously selection)
FLAGs for Watson and Crick strands are now mandatory parameters
PARAMETER NAMES CHANGED (more informative names)
tagW and tagC has been deprecated (new parameters flagW and flagC)
chromSorted has been deprecated (new parameter chromSplitted)
Log output files bug fixed
To ensure directional consistency, the Fisher strand bias is defined as 1 minus the p-value (the higher is the new value, the higher the strand bias)
Multiple FLAGs can be assigned to watson or crick mapped reads (tagW & tagC) - (Thanks to Dr. Krueger for pointing out this pair-end limitation)
Fixed a bug related to perl versions below 5.14 -(Thanks to Dr. Stadler and Dr. Feehery for pointing out this bug)
MethylExtract uses input BAM files without converting the entire file to SAM
MethylExtract_1.3.pl script extracts all detected SNVs (MethylExtractOutMethContexts has been included in the main script).
The memory usage has been reduced.
Default SNVs output is now VCF, check the manual or the output file header.
Default Methylation output retrieves more information and has a more compressed format.
Changed the SNVs calling (similar to varScan), giving more reliable results.
Now the chromosome IDs will be taken from the interval fasta ID (solving compatibility bugs with Bismark aligner).
Missing values in the output files will be filled up with '.' instead of '0'.
Included a script to calculate the bisulfite conversion rate from an unmethylated genome (MethylExtractBSCR_1.2.pl).
Included a script to calculate the error probability for each methylation value and assign a FDR to the entiry dataset (MethylExtractErrorProbability_1.2.pl)
Included a script to extract SNVs and Methylation ratios out of reference methylation contexts (MethylExtractOutMethContexts_1.2.pl).
Included minimum depth parameters ("minDepth").
Improved command line information and help.
Increased log-file information.
All basic functions working.
© Computational Genomics and Bioinformatics Group
Dept. of Genetics & Inst. of Biotechnology
University of Granada, Spain