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The Biostar Herald for Monday, May 06, 2024
Answer: Long reads and fixing of mate-pair issues/marking duplicates with samtools
A: Find consensus overlap between many bed files
Comment: RNA seq analysis
C: What is the best practice of scRNA workflow for multiple patients and samples us
What is the best practice of scRNA workflow for multiple patients and samples using Seurat
Answer: Grouping datasets in Seurat
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Comment: 44% Successfully Assigned Fragments with featureCounts after 85% uniquely mapped
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Wondering, if it was total RNAseq data? or ployA
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It is still obscure to me how many different tissues you would like to include into your comparison and what your intended design is. To …
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred
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Juke34
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You can get a look here https://www.biostars.org/p/9465973/
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A version of the mouse rDNA repeat can be found here: https://www.ncbi.nlm.nih.gov/nuccore/BK000964 Use the dropdown menu at top-left t…
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Christopher
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Hello, Mathew. Firstly, thank you for answering my question. **Sorry, what analysis are you trying to perform with these databases?** I a…
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GenoMax
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As long as it is the same GIAB sample you could compare your SNP with the SNP's available for the whole genome set.
Comment: Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log
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yau
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Dear Mensur, Thanks so much for your reply!! In my case, I got 1 control(healthy) and 2 disease mouse Single cell RNA-sew data, so I …
Comment: BWA alignment
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ATpoint
82k
The relevant code line is precisely the same as in the question.
Answer: imputation through beagle
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dthorbur
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Building a reference panel from the samples you intend to impute seems like a very circular approach. Plus, GBS is a reduced representation…
Answer: Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log
by
Mensur Dlakic
★ 27k
You seem to have too stringent of a p-value cutoff (1e-5). Hopefully you get the concept of how the interplay of `-log10P-value` and `log2F…
Comment: Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log
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yau
• 0
![enter image description here][1] [1]: /media/images/7199a665-b13a-40c8-a065-313cf2b7
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aw7
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This is a bit late, but the first thing to go is to run `samtools --version` and make sure the docker samtools is configured with the the G…
Answer: Long reads and fixing of mate-pair issues/marking duplicates with samtools
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aw7
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I do not think `samtools fixmate` and `markdup` are going to work on PacBio long reads. `fixmate` is for setting and repairing mate inform…
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Azra
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I see, thank you!
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From the perspective of a Chinese, I'd like to choose a letter in a famous journal with a high IF. If I'm a PI, I think they are both OK, I…
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