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Answer: Practical Haplotype Graph v2 not finding correct paths
A: Looking For A Way To Count Total Length Of Regions Of Bed File
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
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Comment: consensus sequence calling
by
bk11
★ 2.4k
Please check out these posts https://www.biostars.org/p/367626/
Comment: Galaxy StringTie error
by
trkfs
• 0
will do, thank you
Answer: Splitting Seurat object by sample layers
by
bk11
★ 2.4k
You can do the following- Idents(SeuratObj) <- "orig.ident" control_set <- subset(SeuratObj, idents = c("counts.control","data.…
Comment: Galaxy StringTie error
by
GenoMax
142k
> I have sent a bug report to the Galaxy administrator If you have not done so please post this in Galaxy help forum for directed help: h…
Comment: 44% Successfully Assigned Fragments with featureCounts after 85% uniquely mapped
by
Thind amarinder
▴ 340
Wondering, if it was total RNAseq data? or ployA
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…
Comment: Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log
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yau
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