User: parvathi.sudha

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United States
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Posts by parvathi.sudha

<prev • 27 results • page 1 of 3 • next >
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Comment: C: How to choose the number of PCs for a large Seurat Object
... Thank you for the help! ...
written 14 days ago by parvathi.sudha20
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How to choose the number of PCs for a large Seurat Object
... I am analyzing a single cell dataset with ~160k cells. The samples were integrated using Reference-based SCTransform. For the downstream analysis, do I have choose a higher number of pcs and dims? Can anyone help me understand how to select the npcs for the runPCA and dims RunUMAP and FindNeighbo ...
scrna seq seurat written 14 days ago by parvathi.sudha20 • updated 14 days ago by rpolicastro3.3k
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Comment: C: Seurat(v3) Integration on multiple dataset
... So in that case, the initial normalization for each sample has to be done using SCTransform. Thank you and sorry for the late reply. ...
written 7 weeks ago by parvathi.sudha20
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Seurat(v3) Integration on multiple dataset
... I am planning to integrate single cell dataset of more than 15 samples with each having 2 conditions using Seurat v3. For this, should I analyze (QC, Clustering etc) each dataset seperately before integrating them? Can anyone suggest the best method to perform this analysis in Seurat? Thanks Pa ...
single cell rnaseq dataset integration seurat written 9 weeks ago by parvathi.sudha20 • updated 9 weeks ago by rpolicastro3.3k
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Comment: C: GTF based salmon index file for GRCh38
... I understood. Thank you! ...
written 4 months ago by parvathi.sudha20
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Comment: C: GTF based salmon index file for GRCh38
... Sorry, I realized that I posted the reply under my initial question. ...
written 4 months ago by parvathi.sudha20
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Comment: A: GTF based salmon index file for GRCh38
... Thank you for the reply. 1) Sure, I will upgrade the tool, I was using the old version as it was already available in the HPC cluster. 2) I will use the full transcript fasta. I didn't completely understand the need for using decoy? If I am just looking for gene level and transcript level expre ...
written 4 months ago by parvathi.sudha20
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GTF based salmon index file for GRCh38
... I am trying to create the salmon index for GRCh38 using Gencode v35. When I did the quantification, even though I added GTF file, "quant.genes.sf is only showing the Transcript id's not gene id's. Can you please tell me how to solve this issue? Is there a way to create a GTF based salmon index file ...
salmon rna-seq index written 4 months ago by parvathi.sudha20
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Answer: A: hsmetrics on_target_bases and on_baits_bases calculation
... Hope, this will be helpful! https://github.com/broadinstitute/picard/issues/476 ...
written 5 months ago by parvathi.sudha20
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Comment: C: how to set the number of segments?
... Hi, I used batch option, and the input target genes were automatically split into multiple regions. I haven't used the --split option. I am curious to know, how you got the results with merged exons. Thanks Parvathi. ...
written 6 months ago by parvathi.sudha20

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Supporter 12 weeks ago, voted at least 25 times.
Popular Question 4.6 years ago, created a question with more than 1,000 views. For Extract list of genes from a KEGG sub pathways

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