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Comment: Demultiplexing bam file
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Pierre Lindenbaum
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> I want to separate every sample
I don't understand. In your header there is only one samples: "`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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dsull
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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…
Comment: Counting intronic reads in bulk RNA-seq
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dsull
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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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Are you sure this is appropriate for bulk RNASeq? I thought intronic reads for single cell were only counted in nuclear preps.
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Are you sure these samples are 10x? How likey is it that the sequencing group messed up and ran the samples wrongly?
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are they distinct transcript IDs but the same gene ID? can you provide any additional context?
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that didn't work either
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Hi @kermit and prash (and others)!
Nice discussion. I wanted to offer some **biological rationales** in addition to the technical reasons …
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There is no `:` after `rule fastqc`
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sorry that was a typo while i was copying my code! I still get the same error
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> fastq.gz".
what is the dot after `fastq.gz" ` ?
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1) I think this is just a warning
2) there must be another error displayed
3) look at samtools view --subsample
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Hello, yes, I tried it, but I have to do my home work on university's remote computer, unfortunatelly I go an error, when I try to use abys…
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