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I've just analaysed a WGS dataset (matched tumor-normal) from a breast cancer sample and the output is telling me that most of the genome is noted as having an increase in copy numbers (CN=3). (see fi…
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Hi Shian,
The latest dorado basecalling models, e.g. dna_r10.4.1_e8.2_400bps_hac@v4.3.0, only support combined 5mCG_5hmCG or 5mC_5hmC for modified basecalling, not just 5mCG as before. However, the…
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From Allison Heath and Eric Wenger:
Good morning, quick question on what the Ontology WG recommends for c2m2 OBI id's in several cases where we are not seeing matches.
Kids First data has several…
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I used cooler 0.7.10-dev version (asymmetric branch) to generate non-symmetric `mcool` file from RNA-DNA interaction `.pairs` data. HiGlass can load the non-symmetric `mcool` file as a non-symmetric h…
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Hello,
I am interested in generating a track that summarizes (using color code) the number of nucleotides aligning at each position. In essence it would be identical to the track that is automaticall…
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Dear msauria,
At the beginning, I must thank you for all your previous supports that helped me on my analysis and exploration. Currently I must build my own nucleosome-resolved contact matrix from …
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`dna_cluster` does many things at once and is not very user-friendly. The different things should probably be accommodated in separate functions. We should think about a clever way to design the overa…
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Hi,this is ZY.We did a summary on the quantity and distribution of CNVs and CNV regions . And I took your advice to visualize the ratio.txt file.But still doubted.
**R script:FREEC_ratio2Absolute.R…
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Dear Olga,
I have now tried different parameters on my dataset. I started with a chromosome-level assembly built from linkage map. The default parameters severely degraded this assembly, which alr…
melop updated
4 years ago