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Hi, Thanks for a quick tool.
I've been using this to UMICollapse my bam files.
Now I want to utilize it on fastq files.
I am confused by the statement:
"fastq: the input is a FASTQ file. This…
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I am working on calling variants in spatial transcriptomics data (10x Visium). Since the sequencing depth of spatial transcriptome is poorer than single-cell data, I want to treat all reads in the bam…
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Hi, developers
I've read the public paper of this program, and downloaded the data. The paper said you used 16x16 UMIs. But I found the UMIs of sequencing data didn't like this type. It seems like …
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Hello, I'm developing a pure Dart application that needs to interact with Google Firestore, and, boy, was I happy when I found your package! I was surrendering to the idea of manually write a conversi…
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Hi!
I am trying to make UMICollapse the default tool in one of the popular RNAseq analysis pipelines -- https://github.com/nf-core/rnaseq/issues/1087.
Not sure if this is covered by #5 already, …
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Hello,
Great article, and very good practice to put the underlying code online in .Rmd.
I could not find the .rds file "ps_umis = readRDS("PulseSeq_UMI_counts.rds")" that is read to the ps_umis…
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Hi, I would like to ask, for the h5ad file input by cellbender, should I use the raw data or the filtered data?
Thank you for your time, thank you!
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Using salmon alevin v1.9.0, I noticed that my *total* reads were less than the deduplicated UMI count when I combined all three libraries together (from a NovaSeq run):
```
{
"total_reads": 2…
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Parameter conflict noticed by @unode
```
EXITING because of fatal PARAMETERS error: --soloUMIfiltering MultiGeneUMI_CR only works with --soloUMIdedup 1MM_CR SOLUTION: rerun with --soloUMIfilte…
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Hi, I used `umis cb_histogram` to calculate reads count for each cell and then chose a count cutoff based on that. For the downstream analysis, such as pseudo-align and count UMI, we only need to deal…