User: biostarukha

gravatar for biostarukha
biostarukha10
Reputation:
10
Status:
New User
Location:
Last seen:
2 days, 2 hours ago
Joined:
10 months, 3 weeks ago
Email:
i****@mail.missouri.edu

Posts by biostarukha

<prev • 19 results • page 1 of 2 • next >
0
votes
0
answers
65
views
0
answers
Reading count martix in scanpy
... 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 ...
scrna-seq python scanpy seurat written 2 days ago by biostarukha10
0
votes
1
answer
54
views
1
answers
Answer: A: Merging previously merged object in Seurat
... 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 biostarukha10
0
votes
1
answer
54
views
1
answer
Merging previously merged object in Seurat
... 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 ...
scrna-seq single-cell seurat rna-seq R written 4 days ago by biostarukha10
0
votes
1
answer
71
views
1
answers
Comment: C: Survival analysis based on a set of genes for TCGA data
... 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 biostarukha10
0
votes
1
answer
71
views
1
answer
Survival analysis based on a set of genes for TCGA data
... 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 ...
R tcga rna-seq survival written 6 days ago by biostarukha10 • updated 6 days ago by Hamid Ghaedi730
0
votes
0
answers
167
views
0
answers
Filtering out mouse cells based on mouse/human genes ratio
... 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 ...
10x rna-seq scrnaseq cellranger written 4 months ago by biostarukha10
0
votes
1
answer
184
views
1
answers
Comment: C: Mapping reads to combined mouse and human genome
... 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 biostarukha10
2
votes
1
answer
184
views
1
answer
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 4 months ago by biostarukha10 • updated 4 months ago by genomax92k
0
votes
2
answers
310
views
2
answers
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 4 months ago by biostarukha10
0
votes
2
answers
310
views
2
answers
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 5 months ago by biostarukha10

Latest awards to biostarukha

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1442 users visited in the last hour