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When I tried running the examples with `--use-singularity`, the runs would fail with `Error in rule mtxs_to_sce_txs` and `Error in rule mtxs_to_sce_genes`. The R log reveals:
```
Error in library(HD…
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### Description of bug
Hi there.
I found two bugs.
1. When running MultiQC `v1.22.*`, the software file pattern `*_mqc_versions.(yml|yaml)` is not being recognised or the file is ignored by som…
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Hello, I am processing single cells obtained by SMARTSEQ. I have created a 3-columns tsv file with cell-id and the two read pairs (`samples`). I launched `kb count` like
```
kb count -t 8 -o $OUTD…
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https://mp.weixin.qq.com/s/4JmnEOvb_d8TVdWpXDDizg
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### Description of feature
One of the issues that repeatedly causes confusion amongst users of the rnaseq pipeline is the reference transcriptome annotation to be provided as GTF or GFF3 (_which is…
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I am interested in separating out my reads that are aligning and not aligning after using kb count. I modified kallisto so that the -n argument is passed. I then run bustools text -f -o bus.txt output…
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Hello everyone. First of all, I'd like to congratulate you on this incredible tool.
In my current project, I need to create cell x transcript matrices for my single nucleus human sample data genera…
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**Describe the issue**
I'm curious as to the result of supp. figure 1.1 in "Modular, efficient and constant-memory single-cell RNA-seq preprocessing". In the presence of a sufficiently long UMI (e.g.…
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Hi guys,
I'm trying to pre-process my fastq file to get loom files. I'm working on mouse models, so I followed kallisto to build index for ref, I split the index into 8 parts (-n 8). When I ran pre…
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The GMM based filtering in mx_filter.py does not seem to work well when there are a large number of cells with a low UMI count.
For a plant root scRNA-seq dataset from[ Shahan et al.](https://doi.o…
harmn updated
2 months ago