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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
Grouping datasets in Seurat
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
Answer: Kraken2 database
Revisiting the FastQC read duplication report
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Comment: RNA seq analysis
by
Matthias Zepper
4.6k
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
by
Juke34
8.6k
You can get a look here https://www.biostars.org/p/9465973/
Answer: Mouse ribosome sequences in fasta format
by
GenoMax
142k
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…
Comment: Kraken2 database
by
Christopher
• 0
Hello, Mathew. Firstly, thank you for answering my question. **Sorry, what analysis are you trying to perform with these databases?** I a…
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
by
GenoMax
142k
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
by
yau
• 0
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
by
ATpoint
82k
The relevant code line is precisely the same as in the question.
Answer: imputation through beagle
by
dthorbur
★ 1.9k
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…
Answer: Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log
by
yau
• 0
![enter image description here][1] [1]: /media/images/7199a665-b13a-40c8-a065-313cf2b7
Answer: Using samtools with GCS (google cloud storage) on a docker container seems to gi
by
aw7
▴ 270
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
by
aw7
▴ 270
I do not think `samtools fixmate` and `markdup` are going to work on PacBio long reads. `fixmate` is for setting and repairing mate inform…
Comment: error in fun(x((i)), ...) : only defined on a data frame with all numeric alike
by
Azra
▴ 10
I see, thank you!
Comment: Publish a Letter in higher impact vs Research article in lower impact
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shenwei356
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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…
Comment: Publish a Letter in higher impact vs Research article in lower impact
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ATpoint
82k
This is off-topic here. I suggest https://academia.stackexchange.com/ Anyway, since hiring procedures in academia are much focused on IF a…
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