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Hello.
How does freebayes deal with overlapping reads (when insert_size is < 2*read_size)? If both reads have the same base in overlapping portion, does it account for non-independence of these two o…
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Hi,
I have found that cleanup_nested.pl doesn't identify the putative copies as belonging to the same family if one of the copy has several non-overlapped blastn HSPs within the other copy the leng…
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When working with the scATAC-seq data for GM12878, I was having poor performance of the models despite using deduplication of the scATAC-seq data like our bulk data. The figure below shows the perform…
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Hi, I understand that the first two columns are the homologs identified via LAST, but I am wondering what the third column (those integer numbers) of .anchor file means.
GSVIVT01012028001 ppa…
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Hi!
First, congrats for your work on Ra and Raven. I've been following and testing your work for nanopore reads for quite a while.
I work in viral genomics (dsDNA viruses), studying new viruses,…
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Hi @marcus1487
I wonder if it could be easy to add info about the position _in the read_ (aside from the position in the reference) for the per-read variant and modification calls. This would be v…
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Hi,
I have the following error in RunGRF.py
```
Fri Mar 20 12:07:28 PDT 2020 EDTA_raw: Check dependencies, prepare working directories.
Fri Mar 20 12:07:52 PDT 2020 Start to find TIR candi…
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Hi.
I tried to investigate the ADs and VAFs of sites with label '0' in the training data.
In most cases, hom-ref sites have very low ADs, which is generated by sequencing errors. However, about 3%…
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Hi Felix,
This is follow-up of my previous [question](https://github.com/FelixKrueger/Bismark/issues/344) about absence of methylation call in ambig_bam output.
So I was so interested in analyzing…
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I tried using Milraa (both released version and development version) on Nanopore reads and the Oxytricha Mac genome from https://knot.math.usf.edu/mds_ies_db/downloads.html. I used the --secondary=no…