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Hello,
When trying to align reads to to the end of a gene, kallisto is unable to pseudoalign this read. However when using the --single-overhang option, pseudoalignment occurs.
My question is …
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An output format that contains counts for all transcripts (in standard order) would be useful for downstream analysis. Like most other quant software (htseq-count, kallisto, salmon)
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Hey,
First of all thanks for this new implementation of the kallisto software with the D-reference you included in your recent paper *"Accurate quantification of single-nucleus and single-cell RNA-…
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Hi,
I have been following this tutorial on generating spliced and unspliced matrices for RNA velocity analysis: https://bustools.github.io/BUS_notebooks_R/velocity.html#generate_spliced_and_unsplic…
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HDF5 libraries version 1.8.4 has different API than what kallisto expects.
From cmake
-- Found HDF5: /usr/lib/libhdf5.so (found version "1.8.4")
after make
/home/vagrant/kallisto/src/h5utils.h:122:6…
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when I build feature using -e parameter,it occurs error information
my kallisto result
![…
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From @cmeesters
> Major Issue:
> here it does not pay out to start with a counting reads rule: there is no motivation to do so. It is not necessary and there is no scientific connection to the DAG…
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1) add a tool to verify strandedness for RNAseq:
https://github.com/betsig/how_are_we_stranded_here
2) Add gene/transcript expression comparison/correlation between stringtie and kallisto
3) ut…
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Is your file,“multi-omic-urothelial-anti-pdl1/analyses/bladder-kallisto-tximport.csv” representative gene expression matrix on each sample ? And is it processed by RNA-seq?
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Hi kite authors,
Thanks for developing a useful tool.
Do you all have a preferred citation for `kite`?
I've already cited `kallisto` and the `bustools` papers, but for `kite` I'm using the Gith…