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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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Recent Replies

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 by Istvan Albert 93k

perhaps the chromosome naming differs `1` vs `chr1`

Comment: Quick Command to Filter Bam Files by 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…

Comment: Error on R shiny app metaOmics; object %AND% not found by Ram 36k

Good catch on the usage! OP should add their experience on that git issue - that issue looks woefully under-detailed.

Comment: FASTA sequence retrieval by GenoMax 115k

> 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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