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Hi Felix,
Another question for you -- I'm looking at M-bias for my samples (8-10x WGBS) and I'm noticing that there is definitely a dropoff of methylation at the start of the read, but it goes back…
caalo updated
6 years ago
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Hi,
When I have been using other RRBS/WGBS methods in the past, I have been filtering out methyalted/non-methyated Cytosines called from less than 10 reads. Is such coverage filtering approach recomm…
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https://github.com/sr320/paper-oly-wgbs/blob/master/submission/Narrative.Rmd#differential-methylation-analysis
sr320 updated
6 years ago
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Where do things stand with an improved Oly transcriptome?
I know @ksil91 sequenced a lot - https://github.com/RobertsLab/project-olympia.oyster-genomic/issues/33
but not sure of assemblies. Is ther…
sr320 updated
6 years ago
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Add the option to rerun the analysis with multiple sample sheets, so that results from the statistical analyses go to separate folders at each rerun.
Try to port this from RNAseq DESeq rule.
First t…
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Hi,
I used this commands:
```
createIndices --local -j 8 --genomeURL /scratch/waterhouse_team/benth/dbg2olc-40x/salsa/scaffolds_FINAL.fasta -o snakePipes-output --tempdir snakePipes-tmp dbg2olc-4…
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Either properly port PlottingID to all the differential statistics or remove/ignore it until further implementation or just store it in the dataframe.
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here: https://github.com/sr320/paper-oly-wgbs/blob/master/submission/Narrative.Rmd#draft-genome-assembly
sr320 updated
6 years ago
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I have two fastq files for a paired WGBS read, as well as hg38.fa.
It's not clear what the sequence of operations is, to go from this, to a SAM or a BAM file. Could you assemble a quick HOWTO or a…
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Hi Felix,
Do you have any perl or C++ script to change bedMethyl to bedgraph (4 column, chr, start, end, mf, only contain CpG position)
Thanks.
Shicheng