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Hi all,
I've been trying to realign some CEL-SeQ2 data: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE157504 The original alignment/counting was performed using zUMIs.
The UMI+BC…
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Hey,
First of all thanks for developing and implementing Kallisto. It is an amazing tool!
I just want to confirm a couple of things regarding the assignment of reads mapping to two transcripts f…
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Hi,
I've download kallisto to install in my new PC using Ubuntu, and it seems I'm not installing the hdf5 and it doesn't let me bootstrap. I've tried to reproduce these instructions: https://pacht…
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Hello,
Thank you for keeping kallisto alive. These days, more and more I realise how its actually important and hard maintain and update tools across many years.
# Background:
I am processing …
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Hi,
I am trying to do velocity analysis in nuclear data, implementing some of the ideas discussed in your paper. I followed some of the steps contained in the scripts from [HSHMP_2022](https://githu…
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I'm trying to perform RNA velocity with kallisto, bustools and their wrapper kb-python following the instructions in [this R Notebook](https://bustools.github.io/BUS_notebooks_R/velocity.html). But I'…
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Hello again,
I am running kallistobustools (`kb`) on BDWTA dataset (mainly, `kb ref` and `kb count`). I was wondering if it is possible to obtain a pseudobam file similar to the one obtained by `k…
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So using the latest version 0.46 (as well as version .45) of kallisto with how_are_we_stranded_here produces this error
`stranded_test_gerald_H3MYFBBXX_1/kallisto_strand_test/pseudoalignments.bam d…
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FileNotFoundError: [Errno 2] No such file or directory: '/tmp/arcas_e8c94069-a619-4cc1-b53c-789445ed2377/pseudoalignments.tsv'
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### Is your feature request related to a problem?
Is there a way to do differential expression of transcripts (e.g. similar to DEseq2 but for transcripts) with RNAlysis?
### Describe the solution yo…