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I'm trying to filter a bam to clamp mod-A to either 0 (canonical) or 100 (modified) so that I can view it in Jbrowse2 showing similar percentages as I am seeing when I summarize the bedmethyl made wit…
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Hi, @ArtRand
I encountered some issues while using modkit extract.
Here is my code:
`${modkitDir}/modkit extract ${bamfile}/input_merge_sup_m6A_pseU.mod.sorted.bam null --read-calls ${bamfile}/inp…
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Hello,
After spending a significant amount of time going through the various modkit threads on how best to set the mod-thresholds and filter-thresholds values, I am still uncertain as to the under…
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Preferred Term: m6A-MTase sequencing assay
Synonyms: Fiber-seq
Definition: A DNA methylation profiling assay in which chromatin stencils are created by treating nuclei with m6A methyltransferase (MT…
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Hi, it is my first time to use Modkit to extract modified base signals but have some problems.
I use Dorado v0.7.1 to do SUP + modification calling (m6A,pseU).
I use minimap2 to align the unaligne…
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Hello,
I have another question concerning this pipeline.
The m6A accessibility and level are calculated using in vitro samples : do you think it is possible to estimate the m6A accessibility in a…
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Hi Dear author,
It says
`We provided sample code in xron-samples folder to achieve m6A-aware basecall and identify m6A site.`
in the document, but I did not find the xron-samples folder in both…
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Hi,
Thanks for this software and hopefully some advice.
There is some evidence of 5-methylcytosine base modifications for my organism of interest (a non-drosophilid fly -- i.e. eukaryotic). More…
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I measured the m6A site values of 46 samples, but I don't understand the significance of coverage in each sample. Is it the number of reads or the peak value of m6A sites at each site? Can coverage be…
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Hi, when i ran gffread, there was a bug.
How should id resolve it.
Thanks.
Code and bug info:
(m6A) [dengy@mu01 00_genome]$ gffread -T Ath_genomic.gff -o 1235
*** stack smashing detected ***: gf…