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Hi Alex
I have a question regarding the output of STARsolo.
In order to process the results in a downstream analysis, I process the output files of the Solo.out folder with the Seurat package in …
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It would be great if a `in_3.fastq` could be specified. A third FASTQ file is often used for single-cell ATAC data to indicate the cell barcode. This third read, is not meant to be be mapped, but the …
ghuls updated
3 years ago
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Hello,
I'm writing because I have recently trialed dropulation on a couple datasets and have found higher doublet rate estimations than anticipated and want to know if some of the parameters that I…
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Dear sir
Hello! Please ask questions about the detectbeadsubstitutionerrors module! Got report Txt, the results are as follows:
![image](https://user-images.githubusercontent.com/67781404/16665233…
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For several datasets I have pulled from the literature, the median UMIs per barcode predicted by `bustools inspect` is much higher than the actual median UMIs per barcode in the output of `bustools co…
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### Description
in the following table definition, the comma of 3 lines:
is_ffpe text NULL -- is_ffpe; Indicator to signify whether or not the tissue sample was fixed in formalin and embedded i…
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**Describe the bug**
Hi there,
I'm having an issue at the "rownames(seurat_milo)
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Hii
While running the Snakemake pipeline, the script stops at
INFO 2021-09-12 23:40:09 BarcodeListRetrieval Looking for the top 5000 cell barcodes
INFO 2021-09-12 23:40:09 BarcodeL…
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Hi, dear wheaton5,
I've met an vartrix error when trying to demultiplex one of my scRNA-seq batches, with following commands:
'./souporcell_pipeline.py -i $POS_BAM -b $BARCODES -f $REF_FAS -t $NUM…
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I am trying to run velocyto run on a non-UMI bam file aligned using STAR. I am using -U flag, however velocyto still tries to find cell and UMI codes and I get the following error: OSError: The bam fi…