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Answer: ScRNA data
by
Dr William Klubinski
▴
10
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
by
GenoMax
129k
> 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
by
GenoMax
129k
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
by
GenoMax
129k
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
by
Pierre Lindenbaum
154k
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
by
alwayshope
▴
20
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
by
Dr William Klubinski
▴
10
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
by
Pierre Lindenbaum
154k
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"`
Comment: Error while running Megahit
by
Mensur Dlakic
★
23k
We can't even begin to guess what the problem was without an error message.
Comment: DEgs RNAseq
by
dsull
★
4.2k
Is this single-cell RNAseq or non-single-cell RNAseq?
For single-cell, you typically don't do standard "differential gene expression analy…
Comment: Counting intronic reads in bulk RNA-seq
by
dsull
★
4.2k
Correct, and I agree -- reads lying fully within introns are usually not counted for either single-cell or bulk.
Inclusion of introns in a…
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