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Forum: Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 3 days ago by 141k • written 3 days ago by • 0
0
votes
0
replies
162
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Forum: Improvement on automatic annotation of single-cell RNA-seq data from the literature using LLM
annotation scRNA llm
3 days ago by yxwucq • 0
4
votes
2
replies
282
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Forum: Bioinformatics: Where do I start
Sequencing
updated 10 days ago by 43k • written 10 days ago by ▴ 10
7
votes
7
replies
1.2k
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Forum: Bioinformatician who was retaliated against after reporting discriminatory harassment - Please help me navigate getting out of the situation I'm in
Career advice
updated 11 days ago by ★ 2.5k • written 11 days ago by • 0
1
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2
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338
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Forum: VCF bulk handling
bcftools SnpEff WGS VEP VCF
9 days ago by Javier • 0
16
votes
10
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1.0k
views
6 follow
Forum: F*up Night style events for Bioinformatics ? Comment if you're interested!
mistakes
updated 28 days ago by 5.3k • written 29 days ago by ★ 2.4k
103
votes
42
replies
31k
views
34 follow
Forum: List of cloud genomics companies
cloud-genomics
updated 17 days ago by 22k • written 10.5 years ago by ★ 3.6k
25
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11
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3.7k
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6 follow
Forum: Site Use Guidelines
meta biostars Guidelines
updated 3 days ago by 43k • written 14.6 years ago by 100k
8 results • Page 1 of 1
Recent Votes
Comment: PCA plot
C: RNA seq library size
RNA seq library size
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
Comment: Convert SAM to BAM
Comment: Should I use unpaired reads from trimmomatic
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Recent Replies
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix by Ram 43k
Simple: ```r data <- lapply(files, read_tsv) data <- Reduce(merge, data) # or Reduce(full_join, data) ``` <a href="" title="Text added bec…
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i by ATpoint 82k
You can make each process use a dedicated environment, see https://www.nextflow.io/docs/latest/conda.html#use-existing-conda-environments …
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix by BioinfGuru ★ 1.7k
Hi, Just thought I'd share this code snippet here for when each file contains multiple samples. I tried using lapply (as suggested by Ram)…
Comment: Low mapping rate with Salmon by i.sudbery 19k
Take your STAR alignment and sum all the counts for each gene. You can either do this by providing an annotation to STAR, or by running fea…
Comment: How to convert plink files to Hapmap Format by bk11 ★ 2.4k
If you run your data with plink 2.0, you will have ERRCODE column in your result file showing the reason behind "NA" p-value. https://www.b…
Comment: genome assembly records not present in assembly_summary.txt by sapuizait ▴ 10
jesus its in the Genbank file and I was looking at the refseq! I m such a moron - thanks for pointing it out -sorry about that :(
Comment: ScRNA data question by bk11 ★ 2.4k
I wonder how the `Vlnplots` will look if you normalize the data using `NormalizeData()` function in `Seurat`. The flat line in your plot ar…
Comment: Low mapping rate with Salmon by GenoMax 141k
> Does that mean that the reads that are not mapped to my trascriptome are not exons/coding genes? Reads are likely aligning in regions wh…
Comment: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File? by cmdcolin ★ 3.8k
the gencode link is broken now but here is a back up of that blogpost on archive https://web.archive.org/web/20130618221342/http://gencodeg…
Comment: Low mapping rate with Salmon by Patadu94 • 0
I'll try to make the decoy file again but I remember you also told me that it is only recommended and not mandatory for running `salmon`. I…
Comment: Low mapping rate with Salmon by Patadu94 • 0
For doing this, should I just look at the log.out.file?
Answer: Heatmap and rna-seq by pinheirofabiano ▴ 10
install.packages("pheatmap") library(pheatmap) setwd("/Users/data_analysis/results") data <- read.table(file…
Comment: Low mapping rate with Salmon by Patadu94 • 0
Thanks for the link GenoMax. But I was wondering, should not alignment and mapping have a similar rate and thus be correlated? In my case I…
Answer: Create a new bed file with all pairwise combinations between two other bed files by Pierre Lindenbaum 161k
bedtools intersect \ -a <(sort -t $'\t' -k1,1 -k2,2n A.bed) \ -b <(awk '{X=250000;P=int($2);printf("%s\t%d\…
Comment: Create a new bed file with all pairwise combinations between two other bed files by J • 0
The command lines I wrote out for you are the ones I actually used. My original reference to bedtools intersect was because I assumed the b…
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