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Answer: High downstream gene expression

Answer: 'SyntaxError': 'return' outside function?

Comment: Analyzing bulk RNA-seq

The Biostar Handbook. A bioinformatics e-book for beginners.

Answer: IGV coverage bar has color, but no mutation?

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Popular Question to amy__ ▴ 50

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Comment: STAR is running but .sam file size does not increase after hours mapping by luzglongoria ▴ 40

If I do df -h then I get Filesystem Size Used Avail Use% Mounted on devtmpfs …

Comment: RNASeq differential expression masked by pathways disregulation by i.sudbery 16k

It you really do have a reason to suspect that the biology of samples from CC1 is different from the biology of samples from CC2, and that …

Answer: High downstream gene expression by i.sudbery 16k

You don't show which species this is. I've taken a quick look at the human and mouse genome at those locations and neither have any genes a…

Comment: Annotating ENS codes to gene name by GenoMax 125k

This is a FAQ, Some past threads linked here: https://www.biostars.org/p/9552097/#9552101

Comment: STAR is running but .sam file size does not increase after hours mapping by GenoMax 125k

You are not running out of storage quota on the particular disk?

Comment: STAR is running but .sam file size does not increase after hours mapping by luzglongoria ▴ 40

I have tried reducing the number of threads but it is the same.

Answer: High downstream gene expression by Matthias Zepper 2.9k

1. Impossible to tell from the information you are showing. Could be misalignments, [read-through transcription][1] ([detection pipeline][…

Answer: Annotating ENS codes to gene name by Apex92 ▴ 240

You can either use biomart to download all gene ids and gene names and then intersect them with your current table. Or you can use your ann…

Comment: CoveragePlot in Signac from MACS2 Object by bioinformatics.girl • 0

This does not work. I called for the gene "Cd8a" for instance for the mouse genome and it says "Gene not found" even though it should appea…

Comment: How to extract the list of genes from TCGA CNV data by Kevin Blighe 84k

Unfortunately it seems that *gaia* has been deprecated. You could still try to install a previous version of it, or set up a new conda envi…

Comment: RNASeq differential expression masked by pathways disregulation by ATpoint 68k

If this is the case then you cannot correct for anything as this effect is nested with center.

Comment: HTSeq error processing GFF file by barslmn ★ 1.2k

That error message is very descriptive. Could you also add the line 997531?

Comment: RNASeq differential expression masked by pathways disregulation by Gama313 ▴ 110

Thanks for the answer. However I am not sure this could be considered batch since CC2 samples have true upregulation of specific pathways t…

Comment: Is the heterozygosity flag (--het) in vcftools calculate observed and expected h by dr.fakharunnisa • 0

Hello #gubrins Have you found the answer

Comment: CoveragePlot in Signac from MACS2 Object by seidel 10k

The `object` will the the Seurat object you're working with, because that contains the data that will be plotted (Tn5 insertion events per …

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