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#SingleCell

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Alberto Perez-Posada

Happy to see out our latest work on studying animal body size variations using single cell transcriptomics to measure gene expression of individual cells. Learned my fair bit of statistics here, and most importantly I learned how to build wrapper functions for "complex" tasks in R (such as differntial gene expression) in a modular way. Thanks to all the authors involved! science.org/doi/10.1126/sciadv #singlecell #scrna #allometry #splitseq #planarians #generegulation

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Eli Roberson (he/him)

#Genomics #SingleCell

These FASTQ files are driving me batty.

I have FASTQ files for a Chromium prepared library. I run cutadapt to try and limit bad reads. I run RNASTAR solo with correct parameters to extract the read UMI and GEM barcode into UM CB tags of BAM file.

I run umitools to dedup based on barcode.

AssertionError: not all umis are the same length(!): 1 - 10

Why. Is umitools. Dying??? All the barcodes and UMIs should be the same length. They're fixed length pulls from the read.

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Eli Roberson (he/him)

Any #rstats #Genomics #SingleCell people used scSplit for genetic demultiplexing of non-hashed mixed samples?

On the GitHub page it says:

"If necessary, remove duplicated reads based on UMI using tools like rmdup in UMI-tools."

github.com/jon-xu/scSplit

That makes sense. But shouldn't it really be by GEM *and* UMI? Just UMI would mix GEMs, and that would exclude identically mapping reads from different droplets. Unless umitools checks *both*. I've only used it on fastq files before, not BAM.

GitHubGitHub - jon-xu/scSplit: Genotype-free demultiplexing of pooled single-cell RNA-Seq, using a hidden state model for identifying genetically distinct samples within a mixed population.Genotype-free demultiplexing of pooled single-cell RNA-Seq, using a hidden state model for identifying genetically distinct samples within a mixed population. - jon-xu/scSplit
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