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Answer: Build canine dna.primary_assembly.fa for kb ref
Comment: Build canine dna.primary_assembly.fa for kb ref
Comment: Difference in total gene counts between samples
Answer: Giotto Error: py_run_file_impl(file, local, convert) : ModuleNotFoundError: No m
Comment: Fasterq-dump unexpected parameter error (unexpected parameter[256]: '/home/GEOda
Answer: Rna Seq Analysis Script
Answer: How to provide read1 and read2 fastq files from two lanes to kallisto | bustools
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Comment: How does salmon deal with decoy?
by
kalavattam
▴ 70
Plain old fasta.
Answer: Build canine dna.primary_assembly.fa for kb ref
by
Candice
• 0
I've found the answer. It turns out the Readme in Ensemble says "If the primary assembly file is not present, that indicates that there are…
Comment: Difference in total gene counts between samples
by
bart
▴ 20
So to be clear, library size is not a factor which can explain the lack of correct clustering in my pcaplots right? So could I use SVA or R…
Comment: What is Nanopore Barcode Score and how is it calculated?
by
henry-keen
▴ 20
I have the same question. Have you figured out this problem?
Comment: Htseq-count: Problem with feature counts
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Istvan Albert
93k
perhaps the chromosome naming differs `1` vs `chr1`
Comment: Quick Command to Filter Bam Files
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Sasha
• 0
Great suggestions!
Comment: Rna Seq Analysis Script
by
GenoMax
115k
Aligners are able to soft clip reads as long as you are aligning to a good reference. So in a strict sense trimming is not necessary.
Comment: Rna Seq Analysis Script
by
Trivas
▴ 250
> You don't need to quality trim RNA-seq. It's actually not recommended in most cases. Can you talk about this some more? This is the firs…
Comment: Build canine dna.primary_assembly.fa for kb ref
by
GenoMax
115k
You should be able to `cat` the files together.
Comment: How to provide read1 and read2 fastq files from two lanes to kallisto | bustools
by
eager_underdog
• 0
Thank you!
Comment: Heatmap making via Complexheatmap package
by
Kevin Blighe
81k
Thank you, but I think that it will still return an error if correlation distance is used.
Comment: Giotto Error: py_run_file_impl(file, local, convert) : ModuleNotFoundError: No m
by
Agatha
• 0
Thank you for your suggestion, have installed it and use a specified python_path to execute the command, yet get this error message: ![en…
Comment: Heatmap making via Complexheatmap package
by
jv
▴ 410
Actually `ComplexHeatmap` has no problem with `NA`s and even has a plotting param, `na_col`, for NA-specific coloring. I routinely plot hea…
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Ram
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Good catch on the usage! OP should add their experience on that git issue - that issue looks woefully under-detailed.
Comment: FASTA sequence retrieval
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GenoMax
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> need to know the functional annotation of each one of them. How to do > it? How to retrieve the fasta seq for a list of genes? You are a…
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