snakepipes: Sample file in WGBS does not produces the appropriate groups
It appears as if names and conditions are all mixed up: Continuing from issue 589 Sample sheet is :
name condition
109242 109242 wt_B73
109243 109243 wt_B73
109244 109244 wt_B73
109245 109245 mut_pht1_6
109246 109246 mut_pht1_6
109247 109247 mut_pht1_6
while running the metillene I found the following that is troublesome:
the following ids belong to group A (n=1): 0: column: 0, name:109242_wt_B73 the following ids belong to group B (n=1): 0: column: 1, name:109243_wt_B73
Group A should have been wt_B73 and GroupB mut_pht1_6
and same for dmrseq:
params = list(NULL, 'dmrseq_BU16_minCoverage5', '/home/hthiele0/snakemake/BU16.txt', c('109242', '109243'), 300, 10, 0.1, 5, 0.1, "blacklist" = NULL, "odir" = 'dmrseq_BU16_minCoverage5', "sampleSheet" = '/home/hthiele0/snakemake/BU16.txt', "groups" = c('109242', '109243'), "maxDist" = 300, "minCpGs" = 10, "minMethDiff" = 0.1, "minCoverage" = 5, "FDR" = 0.1),
So I think that the outputs are not of the correct comparisons
just to add for metilene: from the header of
metilene_BU16_minCoverage5/metilene.IN.txt
chr pos 109242_wt_B73 109243_wt_B73 109244_wt_B73 109245_mut_pht1_6 109246_mut_pht1_6 109247_mut_pht1_6
and then: from header of
metilene_BU16_minCoverage5/DMRs.txt:
chrom start end q-value mean methylation difference nCpGs p (MWU) p (2D KS) mean_109242 mean_109243
About this issue
- Original URL
- State: closed
- Created 4 years ago
- Comments: 18
Hi Theo,
I think your extention is missing a dot ‘.’: --bamExt DOTsortedDOTbam,
Best,
Katarzyna