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Comment: Do bioinformaticians often break molecular biologists' hearts by being the first
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jli.ww
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Based on my personal experience as a computational biologist, I was not a co-first author even if I prioritized the candidates from the pub…
Answer: ScRNA data
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Dr William Klubinski
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It seems like your single cell RNAseq data does not already contain the Cell Barcodes or Unique Molecular Identifiers in the standard way -…
Comment: Demultiplexing bam file
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GenoMax
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> Part of the header of the bam file
So perhaps there are more samples.
https://www.biostars.org/u/21477/: `grep "SM*" header_of_bam`. Is…
Answer: extract all fasta sequence from db v5
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GenoMax
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If you need the fasta sequence download from NCBI here (146 GB zip compressed file) : https://ftp.ncbi.nih.gov/blast/db/FASTA/nr.gz
Comment: ScRNA data
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Is this from a SRA dataset? If so it is possible that you can get the correct information in `DataAccess` tab. Provide the accession number…
Comment: extract all fasta sequence from db v5
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is version 4 compatible with blast v5 ? try to use version 4....
Comment: Does the RNAseq data normal if the TPM value 3rd Qutile expression is near 10, b
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alwayshope
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Thanks a lot! Very helpful detailed guidance! Appreciate it a lot!
Answer: Does the RNAseq data normal if the TPM value 3rd Qutile expression is near 10, b
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Dr William Klubinski
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The values you are getting, with a third quartile of appx 10 and a max of appx 20,000, seem quite standard for RNA-Seq analysis. The RNA-se…
Comment: Demultiplexing bam file
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Pierre Lindenbaum
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you don't talk about the size in your question
Comment: Demultiplexing bam file
by
Pierre Lindenbaum
154k
> I want to separate every sample
I don't understand. In your header there is only one sample : "`13.02.1402_POOL2"`
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We can't even begin to guess what the problem was without an error message.
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Is this single-cell RNAseq or non-single-cell RNAseq?
For single-cell, you typically don't do standard "differential gene expression analy…
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