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**Describe the issue**
kb count INDROPSV2 data [https://data.humancellatlas.org/explore/projects/7c75f07c-608d-4c4a-a1b7-b13d11c0ad31](https://data.humancellatlas.org/explore/projects/7c75f07c-608d-4…
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Hi,
Thank you very much for posting all of the materials associated with this paper and the methods.
In preparation to try and assist with some newly generated ClickTags data, I wanted to first …
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amalgkit quant is terminating without error after encountering file-types it doesn't expect/can't use.
I found 2 different cases so far:
- mismatch in library type and actual data (for example https…
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I’m getting a seg fault during calculating BAM in kallisto quant —pseudobam in version 0.46.2 installed via bioconda. Downgrade to version 0.46.1 and issue the same command works as expected.
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Hi @sbooeshaghi,
I'm trying to quantify multiple paired-end fastq files from single-cell smartseq data similar to what was done in the corresponding publication
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I'm experiencing an issue with qua…
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Overall strategy: sample all reads of cells from a list of cell-ids with known cell-type
- a simple database (e.g. sqlite, even a flat textfile could do it) that stores: cell-id, path to fastqs, ce…
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It would be nice if there were a filter based on the read GC-content as suggested in #76. This filter could be used in addition to the low complexity filter. While the complexity defined in the existi…
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Hi, I have three output files from Kallisto:
1. `abundance.h5`
2. `abundance.txt`
3. `run_info.json`
MultiQC is supposed to be able to read a log file from Kallisto but when I run: `multiqc .`…
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Hi! I was just trying to use the kb tools to get the spliced/unspliced counts for RNA velocity. I was trying to align reads from the FASTQ files: https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-6967/2…
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(Re)running mSWEEP with several clusterings of the reference sequences (eg. hierarchically from genus -> species -> sequence type -> lineage) is sometimes useful but currently requires rerunning the e…