User: biostarukha
biostarukha • 10
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Posts by biostarukha
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... 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
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written 14 hours ago by
biostarukha • 10
• updated
13 hours ago by
genomax ♦ 85k
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... 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
biostarukha • 10
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> 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.
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written 2 days ago by
biostarukha • 10
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... 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 ...
written 2 days ago by
biostarukha • 10
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2 days ago by
swbarnes2 ♦ 7.8k
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... Thank you! The manual said to include certain chromosomes that is why I got confused ...
written 13 days ago by
biostarukha • 10
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... 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, ...
written 14 days ago by
biostarukha • 10
• updated
14 days ago by
khorms • 110
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... 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
biostarukha • 10
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... thank you. Is there any way to use .h5 file instead? ...
written 26 days ago by
biostarukha • 10
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... How to get a GTF file from cellranger output? ...
written 26 days ago by
biostarukha • 10
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... pre-mRNA is a primary transcript that contains both introns and exons ...
written 26 days ago by
biostarukha • 10
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