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v0.18.0 - further NOMe-Seq support and bug fixes
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@FelixKrueger FelixKrueger released this 15 May 10:32
· 542 commits to master since this release
0.18.0
bc3f7f1

Release Notes for Bismark v0.18.0

  • Changed FindBin qw($Bin) to FindBin qw($RealBin) for bismark, bismark_methylation_extractor, bismark2report and bismark2summary so that symlinks are resolved before calling different modules.

Bismark

  • Fixed the behaviour of (very rare) ambiguous corner cases where a sequence had a perfect sequence duplication within the valid paired-end distance.

Methylation Extractor

  • Added new option --yacht (for Yet Another Context Hunting Tool) that writes out additional information about the read a methylation call belongs to, and its output is meant to be fed into the NOMe_filtering script (see below). This option writes out a single 'any_C_context' file that contains all methylation calls for a read consecutively. Its intended use is single-cell NOMe-Seq data, so it only works in single-end mode (paired-end reads often suffer from chimaera problems...)

--yacht adds three additional columns to the standard methylation call files:

<read start> <read end> <read orientation>

For forward reads (+ orientation) the start position is the left-most position wheras for reverse reads (- orientation) it is the rightmost position.

Changed FindBin qw($Bin) to FindBin qw($RealBin) so that symlinks are resolved before calling different modules.

NOMe_filtering

This script reads in methylation call files from the Bismark methylation extractor that contain additional information about the reads that methylation calls belonged to. It processes entire (single-end) reads and then filters calls for NOMe-Seq positions (nucleosome occupancy and methylome sequencing) where accessible DNA gets methylated in a GpC context:

 (i) filters CpGs to only output cytosines in A-CG and T-CG context
(ii) filters GC context to only report cytosines in GC-A, GC-C and GC-T context

Both of these measures aim to reduce unwanted biases, i.e. the influence of G-CG (intended) and C-CG (off-target) on endogenous CpG methylation, and the influence of CpG methylation on (the NOMe-Seq specific) GC context methylation.

The NOMe-Seq filtering output reports cytosines in CpG context only if they are in A-CG or T-CG context,
and cytosines in GC context only when the C is not in CpG context. The output file is tab-delimited and in
the following format (1-based coords):

<readID>  <chromosome>  <read start>  <read end>  <count methylated CpG>  <count non-methylated CpG>  <count methylated GC>  <count non-methylated GC>
HWI-D00436:298:C9KY4ANXX:1:1101:2035:2000_1:N:0:_ACAGTGGT 10 8517979 8518098 0 1 0 1
HWI-D00436:298:C9KY4ANXX:1:1101:5072:1993_1:N:0:_ACAGTGGT 8 9476630 9476748 0 0 0 2

coverage2cytosine

  • Fixed an issue in --merge_CpG mode caused by chromosomes ending in CG.

  • Fixed an issue caused by specifying --zero as well as --merge_CpG.

bam2nuc

  • Fixed an issue where the option --output_dir had been ignored.

filter_non_conversion

Removed help text indicating that this script also did the deduplication.

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