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I receive the following error message when when I try to run TEdenovo on my assembly
```
Fatal error: Exit code 1 ()
cat: /home/jeremy/galaxy/tools/Pipeline/REPET/WORK/genome_Blaster_Grouper_Map/…
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Hi
At the last step of Griffin, I used griffin_merge_sites.py to merge TFBSs for each TF, When I used top 1k sites, everything worked fine, but when I switched to top 10k TFBSs, this script seemed …
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Hello @ArtRand
I would like to confirm that the scores obtained in the DMR are indeed calculated based on the last two columns, i.e., pct_a_samples and pct_b_samples.
Specifically, I would also lik…
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Hello,
I am new to dorado and nanopore datasets. As I was processing the bam file outputs from dorado basecalling from pod5 files, I noticed that for some reads, the length of the move table * str…
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This issue is related to [JOSS](https://joss.theoj.org/) review process track by issue [#7385](https://github.com/openjournals/joss-reviews/issues/7385). Here I'm going to group my comments on the pap…
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Hi, I user Shasta v0.11.1 to assemble a R10.4 dataset, the N50 of the assembly is only 3.4M, is this right? The dataset was download from s3://ont-open-data/giab_2023.05/analysis/hg002/sup/PAO83395.pa…
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Hello,
Firts of all, I would like to express my appreciation for the development of AA. I have been using AA extensively, and it has been a crucial tool in my research.
I am planning to use Hi…
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# Issue Report
## Please describe the issue:
Basecalling of HG002 pod5s using dorado v0.7.2 as part of wf-basecalling results in termination of basecalling for some pod5s. This run has been prev…
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Hi,
I planned to use modkit to calculate methylation entropy, my code is as follow:
```
modkit entropy \
--in-bam ~/nanopore/test.bam \
--base C \
--ref ~/reference/hg38/hg38.fa
```
Well,…
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Dear all,
We have been going through the SAM specification with a fine comb, and
found a few issues.
The main issue is that there seems to be a confusion about ‘read’ and
‘segment’ at various plac…