Comments (1)
PeteHaitch
commented on July 17, 2024
I took another look at the output of bismark_methylation_extractor. In general we can't assume anything about the genomic order of these output files. Processing paired-end data with bismark_methylation_extractor requires that the data are sorted by QNAME, which means that the output is ordered by the order in which it encounters different chromosomes.
from bsseq.
Related Issues (20)
- bsseq object and h5 file HOT 2
- error with the BSmooth HOT 16
- remove common unmethylated CpGs HOT 6
- Error in dmrFinder: 'stat' needs to be a column of 'bstat@stats' HOT 1
- BSmooth error HOT 24
- Error in FUN(X[[i]], ...) : invalid 'type' (character) of argument
- Error in BSmooth.tstat - stopifnot(length(group1) + length(group2) >= 3) HOT 3
- BSmooth error HOT 2
- BSmooth.tstat error, Error in compute.correction HOT 5
- read.bismark() too slow - input format issue? HOT 8
- BSmooth - Error in env[[as.character(i)]] <- value : wrong args for environment subassignment HOT 2
- Error: C stack usage 10847362 is too close to the limit HOT 3
- Is it possible to append metadata to the GRanges within BSseq objects? HOT 3
- Normalization of the WGBS smooth data HOT 5
- bsseq incompatible with tictoc library HOT 1
- Error BSmooth HOT 3
- getMeth relation to CpGs HOT 1
- multiple hypothesis correction HOT 8
- HDF5-backed objects saved with a "prefix" fail to smooth HOT 2
- getCoverage perBase perRegionAverage different outcomes HOT 8
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from bsseq.