User: chilifan

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chilifan70
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Posts by chilifan

<prev • 18 results • page 1 of 2 • next >
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Comment: C: What to think about when treating scRNA-Seq data as bulk RNA-Seq data
... But these suggestions still treat my samples as single cell samples, right? My question regards which pre-processing steps I need to take if I'm just averaging my two samples to contain one vector of gene expression each, and compare these two. Starting out from a digital gene expression matrix. :) ...
written 3 months ago by chilifan70
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What to think about when treating scRNA-Seq data as bulk RNA-Seq data
... We got a bunch of scRNA-seq data and I've done a few tests on them. Now my boss wants me to treat them as bulk RNA-seq data and and compare the differences between treatments. Just as a test. I have not worked with bulk RNA-seq before, so I'm wondering: do you have any opinions on what I should do w ...
scrna-seq bulk rna-seq written 3 months ago by chilifan70
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Comment: C: Unexpected genes in mouse DGE (Digital Gene Expression) (gene-cell expression ma
... That's what is so strange about it! I don't think I aligned to the mixed GTF file, my log says its the mouse, and in the geneinfo i can only see ENSMUS numbers. I'm very confused. ...
written 3 months ago by chilifan70
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Unexpected genes in mouse DGE (Digital Gene Expression) (gene-cell expression matrix)
... Hi! I recently aligned our samples (using STAR and the drop-seq pipeline) to the mouse genome downloaded from the pre made meta data links fund on page 4 in the drop-seq cookbook. Link: https://github.com/broadinstitute/Drop-seq/blob/master/doc/Drop-seq_Alignment_Cookbook.pdf When processing the d ...
drop-seq genome index digital gene expression written 3 months ago by chilifan70
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Singe cell identification library with Ensembl_ID:s
... I am analyzing some gene/cell expression data tor try to annotate the cell type using SingleR. My data is from 10x and consists of two columns that serve as row names, one ensemble Gene_ID and one symbol, for example CYTH3. The data look like below: Gene_ID Symbol AAACCTGCACACTGCG.1 AAA ...
haplotypes ensembl gene_id library annotation written 4 months ago by chilifan70
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Principal component analysis: PC2 contribute more to variance than PC1?
... I am clustering data using Satija's Seurat package. Link: https://satijalab.org/seurat/pbmc3k_tutorial.html Now I'm doing a presentation about principal component analysis (PCA). As I've understood it, the dimensions that contribute with the highest variance to the dataset is used for the first prin ...
pca principal component analysis seurat written 5 months ago by chilifan70 • updated 5 months ago by manuel.belmadani920
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Comment: C: Clusters moving for same dataset and code using tSNE
... Thank you, this makes perfect sense:) I am indeed using another method for clustering, so I conclude that I can trust the cell identities of my clusters then. ...
written 5 months ago by chilifan70
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Clusters moving for same dataset and code using tSNE
... I am clustering data using Satija's Seurat package. Link: https://satijalab.org/seurat/pbmc3k_tutorial.html I am using this exact code and their data, and I generate the same plots as them. However, visualiizing my clusters with tSNE, they are positioned differently compared to the example on satija ...
tsne clustering scrnaseq seurat written 5 months ago by chilifan70 • updated 5 months ago by i.sudbery5.0k
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Chromosome disagreement in drop-seq meta data pipeline
... I am generating meta data and genome index for h. sapiens through the drop-seq 2.0.0 pipeline called create_Drop-seq_reference_metadata.sh. I have tried using fasta reference and GTF files from both ensamble! and gencode (https://www.gencodegenes.org/human/ using the Genome sequence (GRCh38.p12) fa ...
drop-seq rna-seq meta data genome indexing written 6 months ago by chilifan70
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Comment: C: SO:coordinate Error parsing text SAM file. Line: BAM#Pm@HD VN:1.5 SO:coordinate
... Hi @finswimmer thank you for your reply. I started the drop-seq pipeline, but it had an error just before the last step, so I restarted the last step. That is, the first files in the pipeline are generated from this code: >>/home/path/to/tools/Drop-seq-1.12/Drop-seq_alignment_DS.sh -g /ho ...
written 6 months ago by chilifan70

Latest awards to chilifan

Student 5 months ago, asked a question with at least 3 up-votes. For Clusters moving for same dataset and code using tSNE

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