User: biostarukha
biostarukha • 10
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Posts by biostarukha
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... I am trying to read cellranger count matrix using scanpy. The folder 100PDXT contains matrix.mtx.gz, barcodes.tsv.gz, and features.tsv.gz
100PDXT=sc.read_10x_mtx("~/100PDXT/")
when I call 100PDXT.obs, I see cell names, but the shape is 3153 rows × 0 columns.
AAACCCAAGACCATAA-1
AAACCC ...
written 2 days ago by
biostarukha • 10
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... Well, I found the solution. Clustering creates seurat_clusters column in metadata and it messes up with a previous seurat_clusters came from cluster1 and cluster3. So, after merging cluster1 and cluster3, I renamed the seurat_clusters column to 'status'
clusters1_3@meta.data$status <- cluste ...
written 2 days ago by
biostarukha • 10
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... I have two Seurat objects that were made by merging of samples:
object1 <-merge(A, y=B, add.cell.ids=c("A","B"))
object2 <-merge(C, y=D, add.cell.ids=c("C","D"))
For each object I did all preprocessing, PCA, and clustering. Now I want to merge cluster 1 from object1 and cluster 3 fr ...
written 4 days ago by
biostarukha • 10
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... thank you! I did survival analysis for each gene, but only couple of them are significant. So I thought maybe the combination of more genes will be more significant for survival. ...
written 4 days ago by
biostarukha • 10
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... I need to analyze the survival of LUAD TCGA patients depending on the level of expression of a gene set (signature?). I have more than 30 genes for that.
I found this [https://www.biostars.org/p/153013/][1] tutorial. But that is for one gene and KMplot is based on gene alteration rather than low vs ...
written 6 days ago by
biostarukha • 10
• updated
6 days ago by
Hamid Ghaedi • 730
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... I have a 10x output for a tumor sample from a mouse xenograft. To make my further analysis clear, I need to filter out mouse cells. On a cellranger github I found [a similar issue][1]. The developer advised them to map 10x read to a combined mouse-human reference that they have on the 10x website. M ...
written 4 months ago by
biostarukha • 10
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... thank you!
I used cellranger with mouse+human combined reference as you advised. The results say that ~9% reads are mapped to mm10 and ~90% of reads are mapped to hg19. Do you know how to filter out those reads that map to mouse then? ...
written 4 months ago by
biostarukha • 10
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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
...
written 4 months ago by
biostarukha • 10
• updated
4 months ago by
genomax ♦ 92k
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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 4 months 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.
...
written 5 months ago by
biostarukha • 10
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