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Dear Rick,
Thank you for creating this tool. I have run a cDNA gel and want to assess the distribution of my fragments for the purpose of
(long-read) sequencing, as I don't have access to a Bioan…
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Are there any plans to support non-Nvidia GPUs? Like AMD RDNA/CDNA-based ones, or Intel Arc, oneAPI? Also, are there any plans to support GPU virtualization via DPUs (e.g., Nvidia Bluefield or Pensand…
krlc updated
5 months ago
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In my use I add a FASTA asset (a secondary one) like:
```
refgenie build homo_sapiens--GRCh38/fasta:cdna_ensembl95 --files fasta=Homo_sapiens.GRCh38.cdna.all.95.fa.gz
```
That works:
```
>…
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command:
```
kallisto pseudo -i ~/data/cDNA/Homo_sapiens.GRCh38.rel79.cdna.all.idx -o /home/others/xli/scRNA/p20/output2/ --umi -b /home/others/xli/scRNA/p20/output/umi_read_list.txt --pseudobam
``…
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Dear Peng,
I wonder if it is possible to use Deepsignal to detect methylations in RNA from samples sequenced by the direct RNA sequencing kit from ONT.
I think about training a model by using comp…
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Hello,
I was wondering if it is more appropriate to use the v1 standard kallisto index https://github.com/pachterlab/kallisto-transcriptome-indices/releases for bulk RNA seq data compared to an ind…
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Hello,
This is so far a great tool, thanks!
I cannot, however, process proteinvariants in batches.
it works well with a single event:
`transvar panno -i 'PIK3CA:p.H1047R' --refseq`
`input…
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### Description of the bug
When providing several samples that should be mapped to different genomes in a samplesheet, the pairing between sample (group) and genome is ignored.
Expected behaviour…
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One of the engineers on my team noticed that he updated hgvs recently, and after the update we somehow lost the ability to parse cDNA variants with indeterminate nucleotides. Was this by design?
(…
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```bash
ImportError: cannot import name 'run_find_by_type' from 'seqspec.seqspec_find' (/uoa/scratch/users/s14dw4/.conda/envs/cellatlas_fork/lib/python3.7/site-packages/seqspec/seqspec_find.py)
```
…