simpleaf

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[question]: maximum available parallelism and number of threads

1

Hi @rob-p I am trying out this - https://divingintogeneticsandgenomics.com/post/how-to-use-salmon-alevin-to-preprocess-cite-seq-data/ ``` # install via conda conda create -n af -y -c bioconda -c conda-forge simpleaf conda activate af # software installed...

tamuanand

Hi, 10x genomics has developed new technique to detect spatial gene expression of FFPE (formalin-fixed paraffin-embedded) tissue. About 20,000 probes are used to quantify the transcriptome. Cellranger now use the...

wangjiawen2013

Cell-by-isoform matrix

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I wanted to ask if it was possible to generate a barcode-by-isoform count matrix (instead of gene-level counts) using simpleaf; thanks very much.

sameer-aryal

BD data

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@rob-p @robsyme @DongzeHE I have BD (Becton Dickinson) single-cell RNA-seq data that I want to align. Can I do this with `simpleaf`? Thanks

cathalgking

Processing SplitSeq / ParseBio data with simpleaf

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Hi @rob-p and team We have some ParseBio data that it would be nice to process with `simpleaf`. I found this tutorial for `alevin-fry`: https://combine-lab.github.io/alevin-fry-tutorials/2022/split-seq/ It looks like the only...

wmacnair

Hi all, Thanks a lot for building such an excellent eco system of tools, your hard work is very appreciated by everyone in the community :) I've been checking out...

AndrewSkelton

[feature request] 10x chemistry autodetection

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A recurring feature request — provide automatic chemistry detection, at least in the case where we know that the input data is 10x. This would look something like passing `-c...

rob-p

Error: invalid base: 0067

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I'm trying to use simpleaf to build an index for Glycine max (soybean). The genome and gtf files required some preprocessing to get them properly formatted. I ran the following...

holmrenser

Hi @rob-p, hope you're doing well! I have been trying to build an index for the first time in a while, and so I'm returning to an issue that has...

wmacnair

how to do with complex barcodes or multi linked barcode

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Star has the solution: More complex barcodes are activated with --soloType CB_UMI_Complex and are described with the following parameters ``` soloCBposition - strings(s) position of Cell Barcode(s) on the barcode...

d-jch