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A: extract dendrogram cluster from pheatmap

Answer: Counting intronic reads in bulk RNA-seq

Answer: IGV displays genomic coordinates in a 1-based system or 0-based?

RNAseq expression data log2 transformed has negative values.

Samtools: "Too Many Open Files"

Filtering bad quality probes in illumina microarray data

gene filtering for agilent microarray using Limma

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Popular Question to rbaranikumar • 0

Recent Replies

Comment: Demultiplexing bam file by Pierre Lindenbaum 154k

you don't talk about the size in your question

Comment: Demultiplexing bam file by hasani.iut6 ▴ 60

so why the size of bam file is 40 gig?

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…

Answer: Counting intronic reads in bulk RNA-seq by swbarnes2 13k

Are you sure this is appropriate for bulk RNASeq? I thought intronic reads for single cell were only counted in nuclear preps.

Answer: Single cell chemistry by swbarnes2 13k

Are you sure these samples are 10x? How likey is it that the sequencing group messed up and ran the samples wrongly?

Comment: How to deal with duplicated gene IDs in TCGA RNA expression data? by Vincent Laufer ★ 2.8k

are they distinct transcript IDs but the same gene ID? can you provide any additional context?

Comment: SyntaxError (Perhaps you forgot a comma?) in snakefile when running FastQC. by Dhatri Badri • 0

that didn't work either

Answer: Why are some WES VCFs larger than others? by Vincent Laufer ★ 2.8k

Hi @kermit and prash (and others)! Nice discussion. I wanted to offer some **biological rationales** in addition to the technical reasons …

Answer: SyntaxError (Perhaps you forgot a comma?) in snakefile when running FastQC. by WouterDeCoster 47k

There is no `:` after `rule fastqc`

Comment: SyntaxError (Perhaps you forgot a comma?) in snakefile when running FastQC. by Dhatri Badri • 0

sorry that was a typo while i was copying my code! I still get the same error

Comment: too many zeros in 16S rRNA amplicon sequencing data by andres.firrincieli 3.3k

You have too many ASV (40k) and I think this is a problem related to the denoising (DADA2) of NovaSeq 6000 sequencing data. Maybe this post…

Answer: SyntaxError (Perhaps you forgot a comma?) in snakefile when running FastQC. by Pierre Lindenbaum 154k

> fastq.gz". what is the dot after `fastq.gz" ` ?

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