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C: Plotting heatmap of Marker genes in each celltypes in Seurat
C: Plotting heatmap of Marker genes in each celltypes in Seurat
A: Plotting heatmap of Marker genes in each celltypes in Seurat
C: Plotting heatmap of Marker genes in each celltypes in Seurat
C: Plotting heatmap of Marker genes in each celltypes in Seurat
Plotting heatmap of Marker genes in each celltypes in Seurat
Comment: Problem generating paired end reads when converting Cell Ranger's BAM result to
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Recent Replies
Answer: Help with summarizeOverlaps function in RNASeq analysis using R
by
Soheil
▴ 100
I'm guessing you are trying to get the gene expression counts from your BAM files. In this case, I suggest using **featureCounts** from the…
Comment: Database for non cancer cell lines
by
ANSARAHMAD
• 0
Thanks for your response, i will try this method
Comment: Problem generating paired end reads when converting Cell Ranger's BAM result to
by
ATpoint
81k
SRA uses its own nomenclature, while CellRanger reads the original file names. Thats my guess. bamtofastq is save to use, continue with ret…
Answer: Database for non cancer cell lines
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Trivas
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NCBI GEO has started generating RNA-seq counts for publicly deposited RNA-seq studies and GEO2R (see https://www.ncbi.nlm.nih.gov/geo/geo2r…
Comment: Convert to ENTREZGENE
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sansan_96
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Kevin, thank you very much for your valuable help. I am using this output for a KEGG analysis, although I recover very few genes for my ana…
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I0110
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Thanks for your reply, I add the description for data input in the text.
Comment: Problem generating paired end reads when converting Cell Ranger's BAM result to
by
ntuzov
• 0
Thanks for replying. I ran it, but then there is one more question about bamtofastq output (see above).
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48m is tiny, fungal size maybe. HiFi alone should be completely fine. You may not need PoreC on top of that. Start simple and integrate fur…
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There was some discussion with others here https://github.com/WGLab/NanoCaller/issues/21, but I never found an adequate solution - actually…
Comment: Problem generating paired end reads when converting Cell Ranger's BAM result to
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swbarnes2
14k
There's no point in separating lanes 1 and 2. It's fine if they are combined.
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Hello, There is an annotation table for corn / maize (*Zea mays*) at ensembl, accessible via *biomaRt*. What I would do is to first pull …
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This question was also asked on bioinfo SE: https://bioinformatics.stackexchange.com/questions/22331/how-do-i-get-the-gene-annotations-as-a…
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FYI - phgv2 version Release 2.2.68.117 has the updated BioKotlin release with this fix.
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You can do that with https://github.com/brentp/mosdepth as a starting point and then postprocess the output.
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I actually found this to be <s>bad</s> (outdated?) advice. I had no problem to pipe the output of samtools mpileup into an Rscript (R > 4.1…
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