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Hi and thank you for the great tool.
I am trying to perform DEG analysis with DESeq2 and need raw counts. After using kallisto quant my output looks like this:
Since the estimated coun…
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Hello Everybody,
I perform single cell sequencing using droplet microfluidics and barcode cells using barcoded hydrogel beads generated by split and pool technique.
The structure of my library is:
…
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I'm running kallisto vs cellranger on PBMC8k v2.0 chemistry, and it seems that Kallisto doesn't report any mitochondria reads. What could be the reason?
 prints the following:
```
[index] k-mer length: 31
[index] num…
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Hello,
I am trying to run kallisto index using a Singularity image with kallisto 0.51.0.
```
kallisto="kallisto_bustools.img"
ref_fa="gencode.v46.transcripts.fa.gz"
index="kallisto_index/genco…
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WIth typical kallisto pseudoalignment rates of ~70% for human total ribo-depleted RNA libraries, an obvious question is what the remaining 30% of reads represent, especially when aligners like hisat2 …
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p100のkallisto.idxの作成コマンド以下を試しましたがerrorがでました。
kallisto index --index=~/Documents/expression/ref/kallisto.idx ~/Documents/expression/ref/Homo_sapiens.GRCh38.cdna.all.fa.gz
[build] loading fasta file…
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Hello,
This issue is traced back from [my original issue posted for Sleuth](https://github.com/pachterlab/sleuth/issues/175).
The HDF5 output from Kallisto cannot be read by rhdf5 or Sleuth, alt…
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Creating this ticket to evaluate a lighter weight pipeline using [Kallisto](https://pachterlab.github.io/kallisto/) for quantification.
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From @cmeesters:
> [in ep03] we get to named in- and output without explaining the background or that in- and output are usually lists.