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Recent Replies
Answer: nf-core/rnaseq, problem with ensembl reference
by
Kai
•
0
Hello,
This was something that I came across fairly recently. It's somewhat misleading, as it does appear to be an issue with the transcr…
Comment: Which Tool is Better for Genome Polishing Using Illumina and Nanopore Reads: Pol
by
Dunois
★
2.7k
If you've already polished via `Flye` (during the assembly) I doubt it make sense to do long read polishing again after the fact. I'd just …
Comment: The Biostar Herald for Monday, November 04, 2024
by
Dunois
★
2.7k
> The second states that the inflated FDRs reported in the first paper is an artifact of incorrect data generation and that the Wilcoxon te…
Answer: Online Workshop - A Practical Introduction to NGS Data Analysis (December 9-11,
by
ecSeq Bioinformatics
•
0
::LAST CALL:: Online Workshop - A Practical Introduction to NGS Data Analysis (Dec 9-11, 2024) - [Apply Now][1]
[1]: https://www.ec…
Comment: Seurat - unordered cells
by
Bastien Hervé
5.8k
It is hard to say what is "not working" without an overview of what your data look like, or the architecture of your spatial objects.
Do …
Answer: identify transposable elements in iso-seq data
by
lieven.sterck
15k
Hi,
yes, that seems about right what you're doing here.
The only thing I would add is to do a back screen to the non-redundant DB of …
Comment: Seurat - unordered cells
by
solo.albif
•
0
spatial_information (SeuratObject::FOV) is a rather complicated object which contains many other objects (like SeuratObject::Centroids and …
Answer: Creating pathogen test database from nt NCBI
by
GenoMax
146k
You have to obtain the species level taxID's for this to work right. There is a utility program included in `blast+` for this purpose calle…
Comment: I encountered a problem while using Mageck to analysis CRISPR screen data
by
GenoMax
146k
Unless you have a reason to reverse complement the R2 reads (seen a protocol that uses ways so that the barcodes are sequenced in RC orient…
Answer: Need coding help for GO enrichment analysis for non model alga with topGO
by
Dunois
★
2.7k
Take a look at this here: [https://github.com/dadrasarmin/enrichment_analysis_for_non_model_organism][1] .
[1]: https://github.com/d…
Comment: SnakeMake error:
by
Michael
55k
I tried your code literally and I got no syntax error in a dry run. If it was an indentation error, you should see something like
`Indent…
Comment: SnakeMake error:
by
Bastien Hervé
5.8k
Smell like an indentation issue for sure. Try to simplify your script as much as possible (echo something as output, remove your inputs).
…
Comment: Duplication removal of RNA-seq fastq files during the process of annotation
by
dthorbur
★
2.5k
Can you try randomly sampling like 20% of the 200Gb R1 and R2 files? You can repeat this a few times to see how much the permutations are a…
Comment: SnakeMake error:
by
aUser
▴
40
Thank you, I tried with 3 quotes, it gave me same error, however, I changed to singel quote and put the indentation as shown. With this mod…
Comment: SnakeMake error:
by
Bastien Hervé
5.8k
I was wondering if snakemake has a specific interpretation of `"""`, on top of python usual interpretation, which is making multiple lines …
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