User: biostarukha

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biostarukha10
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Posts by biostarukha

<prev • 12 results • page 1 of 2 • next >
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Mapping reads to combined mouse and human genome
... I have single cell RNA seq reads from patient-derived xenograft tumor. I want to see what is the rate of cells with mouse reads. This is my output when I aligned my reads to the human genome: Started job on | Jun 26 11:25:38 Started mapping on | Jun 26 11:27:02 ...
alignment star rna-seq written 14 hours ago by biostarukha10 • updated 13 hours ago by genomax85k
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Comment: C: Filter out mouse reads from single cell RNA-seq of PDX tumor
... I was planning to concatenate mouse and human fasta and gtf files and map my fastq files to those using STAR. But then I saw STAR Log.final.out file and did not see if it distinguishes the cells with mouse reads. > I would think you should be able to spot the cells with mouse reads, so it's pro ...
written 1 day ago by biostarukha10
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Comment: C: Filter out mouse reads from single cell RNA-seq of PDX tumor
... > I would think you should be able to spot the cells with mouse reads, > so it's probably easier to filter at that step. Well, I thought about doing that but I do not know how exactly to remove mouse cells then. ...
written 2 days ago by biostarukha10
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Filter out mouse reads from single cell RNA-seq of PDX tumor
... My goal is to get an expression matrix with gene expression values for each cell without any mouse cells in there. I need to analyze single-cell data from a PDX tumor. I have read papers about the tools for deconvolution of mouse and human genes from PDX tumors. However, I am not sure if they can ...
pdx rna-seq written 2 days ago by biostarukha10 • updated 2 days ago by swbarnes27.8k
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Comment: C: How to generate a mouse reference genome in STAR?
... Thank you! The manual said to include certain chromosomes that is why I got confused ...
written 13 days ago by biostarukha10
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How to generate a mouse reference genome in STAR?
... I am planning to use STAR to map am RNA-seq I have to a mouse genome. I have never done that before. According to the [manual][1], I need to give a path to fasta files. When I looked into [Ensembl][2] database, I found several fasta files for different chromosomes. I would appreciate any opinion, ...
genome mouse alignment star rna-seq written 14 days ago by biostarukha10 • updated 14 days ago by khorms110
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Comment: C: How to remove non protein coding genes from single cell pre-mRNA seq?
... I do not really have a biological background. But I am learning. So, I thought I could ask questions here to get a better understanding of things like that. Thank you for your suggestion though ...
written 25 days ago by biostarukha10
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Comment: C: How to remove non protein coding genes from single cell pre-mRNA seq?
... thank you. Is there any way to use .h5 file instead? ...
written 26 days ago by biostarukha10
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Comment: C: How to remove non protein coding genes from single cell pre-mRNA seq?
... How to get a GTF file from cellranger output? ...
written 26 days ago by biostarukha10
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Comment: C: How to remove non protein coding genes from single cell pre-mRNA seq?
... pre-mRNA is a primary transcript that contains both introns and exons ...
written 26 days ago by biostarukha10

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