User: tujuchuanli
tujuchuanli • 60
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Posts by tujuchuanli
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... Does anyone know how to identify down-regulated genes by monocle? ...
written 18 days ago by
tujuchuanli • 60
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... Hi, all
Here I used “differentialGeneTest” in monocle to identify differentially expressed genes (DEGs) when analyzing scRNA-seq data.
My question is how to mark up/down-regulated genes or there are only up-regulated genes to be identified when using “differentialGeneTest” in monocle? If so how do ...
written 20 days ago by
tujuchuanli • 60
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... Thank you for helpful replying,
There are about 15 paralogs for gene E and 8 paralogs in these are active paralogs. Although the enzyme activity of these 8 paralogs could not be the same. Summing up across these active paralogs could be the best way for me.
I don`t expect that cells with high expr ...
written 5 weeks ago by
tujuchuanli • 60
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... Thanks,
I have edited my post. There are many members for gene E in human genome. Maybe I can call it isoform. However, I don`t mean that these members were generated by different alternative splicing from the same pre-mRNA. ...
written 5 weeks ago by
tujuchuanli • 60
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... Hi,
I am analyzing the scRNA-seq data for breast cancer. Here I want to classify the cells into E+ and E- group which is based on the expression level of gene E (cells with low expression of gene E is E- and cells with high expression of gene E is E+). However, there are several members (isoforms) ...
written 5 weeks ago by
tujuchuanli • 60
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... Hi all,
I am analyzing the scRNA-seq data in Breast cancer. I find that there are 7 clusters in my dataset. I determined cells in these 7 clusters as luminal epithelial cells by expression of marker genes. In one of these clusters, I find that some of ribosome genes are up-regulated when comparing ...
written 10 weeks ago by
tujuchuanli • 60
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Comment:
C: Question about scRNA-seq analysis
... Thanks, benformatics
Actually, I have written a letter to the author and still not have response. However, if they noticed something and excluded it from subsequent analysis, there should be 12 samples instead of 13 samples which were the sample number mentioned in the paper.
...
written 12 weeks ago by
tujuchuanli • 60
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... Hi,
I am interested in the scRNA-seq data from a previous study (http://www.ncbi.nlm.nih.gov/pubmed/31067475). They deposited the dataset under the accession “GSE134520” in GEO dataset. Since they didn`t provide the raw data generated from cellranger, I re-run the cellranger pipeline and do the sub ...
written 12 weeks ago by
tujuchuanli • 60
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... Do you mean that I need all of three files to run "cellranger count"?
The other data in the same dataset, such as "https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR9713123#", contains only two files and the running of cellranger count is just fine using these two files.
Why I use all the three fi ...
written 3 months ago by
tujuchuanli • 60
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... Hi, ale_abd,
Thank you for your replying.
Actually, I tried to convert it from SRA-format to fastq-format using fastq-dump with --split-files. However, it came out to be single-end. Next, if you click the **“Reads” tab** on page https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR9713131. You will f ...
written 4 months ago by
tujuchuanli • 60
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