Tag: Alevin

SALMON Index build Process Killed!

SALMON Index build Process Killed! 0 Hello, I was trying to create an decoy-aware index with Salmon (v1.4.0). So I used primary-assembly genome file and transcript file from Gencode library and followed the steps mentioned in the combine-lab.github.io/alevin-tutorial/2019/selective-alignment. Concatenated transcript file with genome to create gentrome.fa.gz. Then tried to create…

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Tools/pipeline for analysis of smart-seq3 data

Tools/pipeline for analysis of smart-seq3 data 1 I have Smart-Seq3 data and zUMIs refuses to work. Is there any other alternative? Nf-core pipelines rnaseq and scrnaseq doesn’t support sm3 yet. I am also prepared to go down the manual route. Has anyone tried umi_tools or alevin at least to demultiplex…

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Alternatives and detailed information of monocle3

Licence: other No description or website provided. Projects that are alternatives of or similar to monocle3 dropEst Pipeline for initial analysis of droplet-based single-cell RNA-seq data Stars: ✭ 71 (-58.24%) Mutual labels:  single-cell-rna-seq StackedDAE Stacked Denoising AutoEncoder based on TensorFlow Stars: ✭ 23 (-86.47%) Mutual labels:  single-cell-rna-seq kmer-homology-paper Manuscript for functional prediction…

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New Single-Cell ‘Total’ RNA-seq Method Promises More Comprehensive Transcriptome View

This story has been updated to correct information about methods developed by Hao Wu.  NEW YORK – A new method for single-cell RNA sequencing may provide a triple threat: high sensitivity, full-length coverage of RNA, and high throughput. The researchers behind the method — dubbed “vast transcriptome analysis of single cells…

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Quick questions about Alevin and AlevinQC

I have just started using Alevin and I have few basic queries. And I am asking this because I couldn’t find it in the documentation How to know how many reads are uniquely mapping and how many are multi mapping when doing quantification with Alevin. The alevin_meta_info.json says Number of…

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