User: berry
berry • 30
- Reputation:
- 30
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- Location:
- Belgium
- Last seen:
- 1 week, 3 days ago
- Joined:
- 2 years, 5 months ago
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Posts by berry
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... From different papers. They all used GRCh38 but I don't know about the GTF files. ...
written 6 weeks ago by
berry • 30
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... Hi Friederike, thank you for your reply. I only have access to CellRanger outputs unfortunately. ...
written 6 weeks ago by
berry • 30
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... Hi,
I have 3 single-cell RNA-seq datasets from the same platform (10X), same type of sample, same condition, but from different labs to integrate. When I check the genes.tsv or features.tsv files, even though the high majority of the IDs match, I see some differences. For example here "ENSG0000024 ...
written 6 weeks ago by
berry • 30
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... Hi Wei,
Have you find an answer for this question? ...
written 5 months ago by
berry • 30
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... Can you share your email address please? ...
written 6 months ago by
berry • 30
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... Sorry Antonio I was confused. So I got `760257.6` for the columns. And I guess this means it is already TPM?
This was a public data and it was very hard to get a clear answer from the authors.
Thank you for your help :) ...
written 6 months ago by
berry • 30
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... Hi António,
Thank you very much for your reply.
When I sum up the columns, I got this : 760257.6
So I tried transforming with 2^(log(TPM+1)) and then summing up the columns I got this : 157130.48
Do you have any idea why this could be happening? ...
written 6 months ago by
berry • 30
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... Hi,
I have been given a normalised count matrix (single-cell) as following :
Cell1 Cell2 Cell3 .....................
Gene1 0.0000 0 0.0000
Gene2 0.0000 0 0.0000
Gene3 155.8516 0 0. ...
written 6 months ago by
berry • 30
• updated
6 months ago by
antonioggsousa • 2.0k
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... Thank you very much, I appreciate it. ...
written 9 months ago by
berry • 30
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... Thank you for your reply.
My version is 2.17.1 and that doesn't accept sample.type = "Primary solid Tumor". It works with "Primary Tumor".
With your code, I'm only able to download "hg19.seg" file. However, I want to download a different type of segment data that is processed with ASCAT2 and fil ...
written 9 months ago by
berry • 30
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