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-1 votes

Multiple genome assemblies of the same bacterial species

What I would suggest, without knowing much biology about the system is it's a tree problem. The difficulty is knowing whether the repo is prokaryotic. To solve it I'd take the 16S gene and make a tree ...
M__'s user avatar
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1 vote

Bedtools genomecov gives me coverage files showing zeros at all nucleotide positions

option -pc is for -pc Calculate coverage of pair-end fragments. but your reads are single-end reads
Pierre's user avatar
  • 1,511
0 votes

After running nf-core, is there a way to map a gene_id to a specific gene's DNA sequence?

fishing out tp53 RNA-Seq reads go to NCBI Taxonomy Browser put Anas platyrhynchos as a search term click on Anas platyrhynchos ...
darked89's user avatar
  • 293
0 votes

Salmon Multiple File SCRIPT giving error

Are you sure the find operations return exactly one file each? The error seems to state that there were no files found for some run. Or it could also be that you ...
Ram RS's user avatar
  • 2,299
1 vote
Accepted

WGCNA: Extract genes within the different modules to create a dataframe with two columns

You can get this information, more or less, using the functions exportNetworkToVisANT and exportNetworkToCytoscape. You will find some extra columns that you can ignore or delete from the resulting ...
Peter Langfelder's user avatar
1 vote

How to normalise Bulk RNA-seq data to account for transcript length, coverage depth, library size and batch effects?

Have a look through the DESeq2 manual. It goes into a lot of detail about how it works, and how you can use it to do all the things you're asking about: https://www.bioconductor.org/packages/devel/...
gringer's user avatar
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2 votes

How to normalise Bulk RNA-seq data to account for transcript length, coverage depth, library size and batch effects?

All factors you mention bar the batch effects can be addressed by some sort of normalization (I use a modified version of UQpgQ2). Batch effects can be addressed using ComBat/SVA/ComBat-seq but my ...
Ram RS's user avatar
  • 2,299

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