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This came up in #336
When building a gencode-based index with `salmon index` without the `--gencode` flag, the index that is generated won't work when subsequently running e.g. `salmon alevin`. Thi…
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Per the [Alevin documentation](https://salmon.readthedocs.io/en/latest/alevin.html): alevin needs a genes_2_tx mapping file that does not have a header. As of now, we have ready made genes_2_tx files …
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In biology, there can be some duplication (won't go into detail here). However, in our lab processes, when we create sequencing data we also create _technical_ duplication, which we want to ignore in …
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Hi, I've updated a little bit regex code for ddseq/surecell, because I think it's not optimal that one, which is in your FAQ - it's missing information about possibility of the PhaseBlock at the begin…
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Now that we had to update Salmon so we could use Alevin, we also need to remake the previously made Salmon index, because it is not compatible with the newer Salmon version.
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An epic to group the tickets to report on .
- [ ] Requested information on current status of Optimus - what is in the pipeline now, demo of pipeline
- [ ] Requested focus on delivering comparison of …
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**Is the bug primarily related to salmon (bulk mode) or alevin (single-cell mode)?**
**Describe the bug**
A clear and concise description of what the bug is.
**To Reproduce**
Steps and data to…
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1: All repositories with a minor update, like Alevin (908a8d400fa2)
will be turned i…
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Hi,
I've been trying to run alevin for single cell data. I've been using test data and the salmon alevin command seems to work right until the end, and then the core is dumped just as counts are in …
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**Is the bug primarily related to salmon (bulk mode) or alevin (single-cell mode)?**
Affects salmon (bulk mode) for sure. I don't know alevin.
**Describe the bug**
totalCount_ is not initialized …