Tag: mkref

A transcriptomic taxonomy of mouse brain-wide spinal projecting neurons

Animals All experimental procedures were performed in compliance with animal protocols approved by the Institutional Animal Care and Use Committee at Boston Children’s Hospital (Protocol no. 20-05-4165 R). Mice were provided with food and water ad libitum, housed on a 12-hour light/dark schedule (7 a.m.–7 p.m. light period) with no more than five mice…

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Different “Reads Mapped Confidently to Transcriptome” values in scRNA

Hello everyone. My question is about sing-cell RNASeq. I am re-analyzing a scRNA raw data in my lab, which has previously analyzed by seqencing company, i am trying to replicate the results and update/optimize my pipeline. Currently my pipeline is as follows: 1. Creating custom reference I indexed the reference…

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Creating custom GTF file for use with Cellranger with barcode sequences

Creating custom GTF file for use with Cellranger with barcode sequences 0 Hello all I am working with 3′ single cell expression data that has been generated on the 10x Chromium platform. The starting material is human cells that have been labeled with an RFP expressing lentiviral vector which also…

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feature.tsv from scRNA-seq dataset has gene name with dash number suffix following adopting NCBI reference

feature.tsv from scRNA-seq dataset has gene name with dash number suffix following adopting NCBI reference 1 Hi, I’m a user of scRNA-seq in veterinary medicine field. like scRNA-seq analysis. Yesterday, I got fatsq files, and using these I ran a cellranger count with the canine reference genome canfam6.0, a newly…

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Ubuntu exits (Cellranger mkref, custom reference)

Hello, I am trying to generate a custom mouse reference genome that includes 3 transgenes (eGFP, tdTomato, and Cre), I have added these to the reference genome and the gtf as well as filtered the gtf with no issues. When I run mkref (usung Ubuntu within windows, version 2204.2.33.0), it…

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Create customized gene annotation file

Create customized gene annotation file 0 Hi, I have self-defined RNA sequence, it was used to tag the special cells I’m interested in. I want to use cellranger mkref to build a custom reference and use this reference file to count the cells that have this sequence. Do you have…

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Somatically hypermutated antibodies isolated from SARS-CoV-2 Delta infected patients cross-neutralize heterologous variants

Data reporting No statistical methods were used to predetermine sample size. The experiments were not randomized. The investigators were not blinded to allocation during experiments and outcome assessment. Study approval This study and all the relevant experiments were approved by Guangzhou Eighth People’s Hospital Ethics Committee (No. 202001134 and 202115202)….

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transcriptome – How to combine multiple .fasta files of primary assembly from Ensembl into one for sequence alignment?

I have some marmoset snRNA reads that I want to align with the reference transcriptome using cellranger. The primary assembly for marmoset is available here, which is broken down into 22 parts. However, cellranger mkref only accepts one .fa file to generate the transcriptome. I tried concatentaing all the extracted…

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Your reference doesn’t appear to be indexed. Please run the mkref tool.

cellranger-dna: Your reference doesn’t appear to be indexed. Please run the mkref tool. 1 I received the following error when running cellranger-dna: “Your reference doesn’t appear to be indexed. Please run the mkref tool”. The reference that I used was downloaded from 10X database. I thought the reference was already…

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