User: tofukaj

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tofukaj10
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10
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New User
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Last seen:
4 months ago
Joined:
3 years, 3 months ago
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t******@gmail.com

Posts by tofukaj

<prev • 15 results • page 1 of 2 • next >
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Comment: C: Is it valid to use differential gene expression analysis tool for scRNA-seq with
... More significant genes acquired. ...
written 4 months ago by tofukaj10
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Is it valid to use differential gene expression analysis tool for scRNA-seq with bulk RNA-seq data?
... Dear all great helpers, As indicated by the title, I'm wondering if it is valid to use differential gene expression analysis tool for scRNA-seq with bulk RNA-seq data. I curiously tried applying MAST package with the low input RNA-seq data of my interest. It rendered me better results than those ac ...
rna-seq written 4 months ago by tofukaj10
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Comment: C: Drop-seq cell barcode whitelist
... Thank you very much!! ...
written 4 months ago by tofukaj10
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Comment: C: Drop-seq cell barcode whitelist
... Dear Kevin, Would you please enlighten me a little bit more? **After STARsolo alignment, how could you acquire the expression matrix of all cells of a file?** I have tried `--quantMode GeneCounts`, however it rendered me the overall gene counts of the sam file not gene count per cell. Best regards ...
written 4 months ago by tofukaj10
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Comment: C: Drop-seq cell barcode whitelist
... Thank you very much!! ...
written 4 months ago by tofukaj10
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Comment: C: Drop-seq cell barcode whitelist
... Dear Kevin, **Would you kindly tell me if you successfully apply STARsolo with Drop-seq?** I also plan to learn how to use STARsolo with Drop-seq analysis. **It would be very kind of you if you can provide me an example for such application.** Best regards, Kaj ...
written 4 months ago by tofukaj10
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Answer: A: Please help : How to deal with 'Missing gene_name' of GTF file?
... According from all your kind suggestions, I've managed to create new gene_name and transcript_name using gene_id and transcript_id. This could be achieved by 'pygtftk' (https://github.com/dputhier/pygtftk). Assoc. Denis Puthier-whom I gave the overall credit to him kindly provided me guidance as fol ...
written 4 months ago by tofukaj10
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Comment: C: Please help : How to deal with 'Missing gene_name' of GTF file?
... Thank you very much!! ...
written 4 months ago by tofukaj10
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Comment: C: Please help : How to deal with 'Missing gene_name' of GTF file?
... That's a brilliant idea! However, my very poor coding skill will never get me to that solution. Is it possible to have a code to fill the missing gene_name in these line with their gene_id? ...
written 5 months ago by tofukaj10
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Comment: C: Please help : How to deal with 'Missing gene_name' of GTF file?
... Thank you very much for your kind advice. I have tried download the canine GTF file from UCSC. It cannot be applied with the ConvertToRefFlat function of Drop-seq tools. I would try to ask the maintainer about this. ...
written 5 months ago by tofukaj10

Latest awards to tofukaj

Scholar 4 months ago, created an answer that has been accepted. For A: Please help : How to deal with 'Missing gene_name' of GTF file?
Popular Question 23 months ago, created a question with more than 1,000 views. For Removing rRNA,tRNA,snoRNA, etc from miRNA sequence data

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