User: pomodoro_sinensis
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Posts by pomodoro_sinensis
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... According to the SCVI tutorials, it is recommended to pre-select highly variable genes before training the SCVI model. Here is a piece of the code from here: https://docs.scvi-tools.org/en/stable/user_guide/notebooks/harmonization.html
adata.layers["counts"] = adata.X.copy()
sc.pp.normalize ...
written 12 days ago by
pomodoro_sinensis • 0
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... Hi Juke34. It seemed like it wasn't working but it ended up running! It was just that it took very long (~5 hours). Here is the output I got from that section:
--------------------------- Check4: l2 linked to l3 ----------------------------
88226 cases fixed where L3 features have parent fe ...
written 22 days ago by
pomodoro_sinensis • 0
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... Thank you so much!! If I may, I am going to paste the question I made to rpolicastro on the same topic:
Thank you! Yes, that is exactly what I needed. However the function does not seem to be working for me. Here is the output that I get after executing it:
Filtering ontology:
We fou ...
written 23 days ago by
pomodoro_sinensis • 0
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... Thank you! Yes, that is exactly what I needed. ...
written 23 days ago by
pomodoro_sinensis • 0
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... I have a gtf file that looks as follows (lines for transcript ENSMUST00000027477):
protein_coding exon 87510093 87510362 . - . gene_id "ENSMUSG00000026259"; transcript_id "ENSMUST00000027477"; exon_number "1"; gene_name "Ngef"; gene_biotype "protein_coding"; transcript_name "Ngef-002"; exon_id ...
written 23 days ago by
pomodoro_sinensis • 0
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... I am working with a scRNA-seq count matrix from a paper whose genes have names as follow:
213 1700022K14Rik
214 1700022N22Rik
215 1700022P22Rik
216 1700023E05Rik
217 1700023F06Ri
...
1802 AC158802.1
1803 AC158997.1
1804 AC161214.1
. ...
written 5 weeks ago by
pomodoro_sinensis • 0
• updated
5 weeks ago by
ATpoint ♦ 46k
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Comment:
C: Unable to find this E coli genome
... Here is an example of a B subtilis file for cDNA (corresponding to the other genome that appears in my initial message).
ftp://ftp.ensemblgenomes.org/pub/bacteria/release-49/fasta/bacteria_0_collection/bacillus_subtilis_subsp_subtilis_str_168_gca_000009045/cdna/Bacillus_subtilis_subsp_subtilis_str_ ...
written 6 weeks ago by
pomodoro_sinensis • 0
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C: Unable to find this E coli genome
... Thanks so much!!
I know there are no introns in bacteria, but still cDNA is not the collection of CDSs, am I right? A 5' or 3'UTR is part of the cDNA but not of the CDS. Is it called CDS because it doesn't include those sequences? Or is it just the way of calling the cDNA (UTRs and CDS) in bacteria' ...
written 6 weeks ago by
pomodoro_sinensis • 0
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Comment:
C: Unable to find this E coli genome
... Also, where did you click here: https://www.ncbi.nlm.nih.gov/assembly/GCF_000800765.1/
to get to the full directory? ...
written 6 weeks ago by
pomodoro_sinensis • 0
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C: Unable to find this E coli genome
... Wow thank you!! Do you happen to know why there is no transcriptome in the full directory? (i.e. a cdna.all.fa file) Or is it me who is not finding it? ...
written 6 weeks ago by
pomodoro_sinensis • 0
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