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Dear developers;
Thanks for the great tool for variant calling. I use deepvariant 1.6.1 for small variant calling from picbio HIFI data (Revio system). For HIFI data, there are two ways to get th…
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Hi,
I am using methphaser as a singularity image on an HPC. I have made the singularity image work with the test data, so shouldn't be any technical issues with the image.
I am doing adaptive se…
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Hello,
the Debian Med team is maintaining nanopolish for official Debian. The recently released Debian 10 was the last Debian release featuring Python2 since this programming language is EOL. If …
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I have been using TEcount for estimating TEs in total RNA-seq data which has worked great. However, I want to combine this with methylation data and there we have methylation differences at the transc…
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Hi teacher ! I'm trying to call DNA modifications by using deepmod.However,i get the problem 'Error information for different fast5 files: Not in alignment sam 1095'.Can you give me some advice about …
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Hello. Thank you for creating this useful tool! I called mC and hmC bases, aligned the .bam files, sorted and indexed, and then created bed files. Then I wanted to perform modkit dmr pair on my two sa…
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Hi Michael and the team,
thanks a lot for the tool and for the recent update to 4.0.3. I am currently working with heavily 5mCG methylated DNA samples (in vitro methylation) and I was planning to a…
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While the actual imputation time is very short using a GPU (as observed on nvtop), the mixgb processing time is prohibitively long: it takes about 3-5 minutes per column before the GPU kicks in. My da…
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Fang Lab,
Unfortunately the singularity installation option wasn't working for for our campus cluster or my lab machines. As such, I had to set up a conda environment on our cluster and attemptted …
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As noted in point 1 here: https://github.com/broadinstitute/tensorqtl/issues/68
> there will be >400K CpG sites in the data compared to >20K genes. What would you suggest be a good cis_window for a…