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metheor looks like exactly the tool I need, however I am not using bisulfite data as input. I called methylation directly using nanopore sequencing and my .bam files store it with MM and ML tags accor…
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I ran the example in https://nanopolish.readthedocs.io/en/latest/quickstart_call_methylation.html.
However, I noticed that some reported coordinates were not pointed to C/G base and probably shift -1…
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While using dnmtools (v 1.2.4 by command line) mlml with mock bisulfite and oxidated bisulfite data. Some, but not all, samples yielded this error:
error: chrom or pos mismatch in both files
The i…
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Hello Maarten,
I have questions concerning the paramenters you use for demultiplexing.
If I understand correctly you do not allow mismatches in the barcode (--barcode_dist 0) and you do not disa…
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Now may be a good time to assess resource usage of the bisulfite pipelines, when a variety of samples are being processed in relative proximity. The pipeline interface could be updated to reflect obse…
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Hi!
I am trying to do overlaps over all the Bisulfite dataset, when I subset for a specific cell type, the analysis goes without any problem, but if I choose all the cells with 100 permutations, th…
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Dear authors,
Thank you for creating accel-aligner. It is very fast and sensitive in my tests.
I have been trying to apply accel-aligner to bisulfite sequencing reads and was able to successful…
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Hi,
these days, i analysis bisulfite sequencing using BSseeker2.
but some target reads are aligned to multiple location of genome.
so i want to know where is this region.
what can i do?
Bes…
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### Description of feature
Library preparation kits come with unmethylated and methylated DNA controls that are added to samples (e.g. NEBNext EM-seq). It would be useful to supply methylseq with the…
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Dear Bismark Author,
I was running my data with the bismark tool and i got the error message below. the version of bismark is: version v0.24.2 and the code i used to run is:
/home/jkalami/.conda/env…