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1,000 results • Page 3 of 20
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4
votes
14
replies
2.6k
views
Is it possible to annotate single genes by snpeff
snp vcf
updated 10 months ago by 43k • written 6.7 years ago by ▴ 70
4
votes
13
replies
866
views
RNAseq of primary tumor and metastases in two different organ
metastases RNA-seq DEG R
updated 9 days ago by ★ 1.7k • written 15 days ago by • 0
4
votes
2
replies
624
views
Visualization package for Maf Files using Python
Python maftools Visualization MAF
updated 6 months ago by ★ 1.5k • written 6 months ago by ▴ 100
4
votes
3
replies
751
views
Creating custom GTF file for use with Cellranger with barcode sequences
Cellranger
7 months ago by stefano.iantorno ▴ 70
4
votes
9
replies
572
views
variant calling
variant-calling
updated 23 days ago by 43k • written 24 days ago by • 0
4
votes
4
replies
603
views
Request for a linkage analysis tutorial
linkage
updated 8 months ago by 141k • written 8 months ago by ★ 2.9k
4
votes
8
replies
3.5k
views
How to reduce the number of SNPs for the Lositan software
Lositan SNP
updated 10 months ago by 43k • written 9.5 years ago by • 0
4
votes
7
replies
811
views
SNP IDs
SNP
5 months ago by kl ▴ 10
4
votes
3
replies
305
views
Should you remove PCR duplicates for kmer counting?
kmer dedup duplicates
updated 11 weeks ago by 4.6k • written 11 weeks ago by ▴ 30
4
votes
7
replies
2.2k
views
About normalization of the datasets from Harmonized TCGA data
protein transcript normalisation
updated 11 weeks ago by 43k • written 21 months ago by ▴ 10
4
votes
2
replies
560
views
Can I still remove ambient RNA if I do not have raw barcode-gene matrix?
SoupX
6 months ago by malonzm1 ▴ 20
4
votes
6
replies
2.1k
views
Single nucleotide Polymorphism (SNP)
SNP
updated 10 months ago by 43k • written 9.0 years ago by ▴ 10
4
votes
7
replies
1.4k
views
.bed files from sequencing platform not containing intervals of "alt", "random" haplotypes. How do I perform coverage and haplotype caller?
exome .bed haplotypes HG38 coverage
updated 9 months ago by 141k • written 9 months ago by • 0
4
votes
9
replies
1.2k
views
Snakemake issue with wrappers
Python Snakemake
5 months ago by Begonia_pavonina ▴ 150
4
votes
6
replies
804
views
how to plot SV(structural variants) from many assemblies of a given locus
SV
11 months ago by natalev ▴ 20
4
votes
4
replies
794
views
Segmentation fault Biopython pairwise alignment
biopython alignment
updated 11 months ago by 21k • written 11 months ago by ▴ 20
4
votes
2
replies
229
views
Trying to write bwa mem -> samtools view -> samtools sort loop
bwa samtools mapping genome
updated 21 days ago by 161k • written 21 days ago by • 0
4
votes
6
replies
2.6k
views
Convert Nanopore Fast5 files to Fasta format
fast5 fasta Nanopore
11 months ago by Sowmya Pulapet ▴ 70
4
votes
6
replies
339
views
Protein loops
protein Loop
6 weeks ago by Curious ▴ 10
4
votes
8
replies
607
views
GCP Snakemake
snakemake GCP
updated 3 months ago by 43k • written 3 months ago by ▴ 10
4
votes
6
replies
933
views
How to pass from DNA to AA fasta
genetics
updated 11 months ago by ★ 2.4k • written 11 months ago by • 0
4
votes
2
replies
2.2k
views
Bfast Match Paired End Reads - Reports Half Total Number Of Reads
paired-end alignment next-gen
updated 10 months ago by 43k • written 11.3 years ago by ▴ 50
4
votes
6
replies
1.0k
views
Python script to automatically read in, name output files & parse R1 & R2 fastq.gz files when given an input directory with raw data files
python fastq
9 months ago by eorr ▴ 30
4
votes
6
replies
835
views
bwa mem hangs after a few thousand reads
bwa alignment variant-calling bwa-mem
updated 24 days ago by 43k • written 4 months ago by ▴ 30
4
votes
8
replies
1.9k
views
Hello, I have differential ATAC-seq from control and diseased cells (H3K27ac mark as chromatin mark) and wondering how to call enhancers using ROSE …
super-enhancers Enhancers
updated 12 weeks ago by ★ 16k • written 3 months ago by • 0
4
votes
5
replies
536
views
Which refseq_protein db to choose for zingiberaceae
local blastp blast
updated 8 months ago by 141k • written 8 months ago by • 0
4
votes
4
replies
604
views
I cannot install anaconda on ubuntu 22.04
ubuntu anaconda Conda
updated 8 months ago by 43k • written 8 months ago by ▴ 10
4
votes
5
replies
778
views
Does adding reads cause batch effects?
kallisto RNAseq
10 months ago by bioinfo ▴ 150
4
votes
7
replies
798
views
Help with weighted nearest neighbor analysis
seurat single-cell
8 months ago by Chris ▴ 260
4
votes
5
replies
1.0k
views
VEP run with --af_gnomadg refuses to provide allele frequencies for extremely rare variants
vep gnomad
updated 8 months ago by ▴ 60 • written 8 months ago by 22k
4
votes
4
replies
847
views
retaining only the clusters of interest
seurat single-cell scRna-seq
updated 10 months ago by 43k • written 10 months ago by • 0
4
votes
3
replies
483
views
Parsing columns with awk
awk
updated 5 months ago by 43k • written 5 months ago by ▴ 300
4
votes
12
replies
3.5k
views
How to read VCF (v4.1) file? (student project) (samtools version 0.1.19)
variant-calling samtools VCF BCF
updated 4 weeks ago by 43k • written 5.5 years ago by ▴ 110
4
votes
6
replies
632
views
Unexpected separation of RNA-seq samples on PCA plot
depletion PCA rRNA plot RNA-seq
5 months ago by Tihana ▴ 10
4
votes
16
replies
1.7k
views
How to subset large BAM files specifically/ extract specific subsets?
bamtools RNAseq samtools BAM
updated 9 weeks ago by 43k • written 7 months ago by • 0
4
votes
3
replies
309
views
Getting less DE genes when incorporating all samples
RNA-seq differential-expression deseq2
updated 10 weeks ago by ★ 1.8k • written 10 weeks ago by ▴ 10
4
votes
9
replies
1.0k
views
bcl2fastq troubleshooting all reads dumped to "Undetermined"
demultiplex illumina sequencing
updated 4 months ago by 141k • written 4 months ago by ▴ 120
4
votes
6
replies
1.2k
views
Transcript quantification
rna-seq transcriptome SRA
updated 10 months ago by 82k • written 10 months ago by • 0
4
votes
1
reply
624
views
How to interpret Clustree results?
scRNA clustering clustree
updated 8 months ago by 3.9k • written 8 months ago by ▴ 120
4
votes
11
replies
1.6k
views
Check Strandedness
Check_Strandedness how_are_we_stranded_here leafcutter bash
updated 6 months ago by 20k • written 8 months ago by • 0
4
votes
7
replies
1.0k
views
Statistical test to compare data across timepoints
Statistics
updated 6 months ago by 4.5k • written 6 months ago by ▴ 20
4
votes
4
replies
645
views
Feedback on mouse brain scRNA-seq quality control
mouse brain singe-cell scRNAseq quality-control
8 months ago by nshenoy ▴ 50
4
votes
8
replies
2.0k
views
How to extract promoter sequences from a plant draft genome?
promoter genome
updated 10 months ago by 43k • written 4.6 years ago by ▴ 120
4
votes
11
replies
1.8k
views
PCA WITH PLINK
PLINK
updated 8 months ago by 87k • written 8 months ago by • 0
4
votes
6
replies
955
views
Open-Source software. Good or bad for the market?
genomic-analysis software
updated 11 months ago by 43k • written 6.2 years ago by • 0
4
votes
5
replies
1.4k
views
Distributed / parallel computing in bioinformatics
distributed-computing
updated 11 months ago by 43k • written 6.8 years ago by ▴ 750
4
votes
3
replies
1.0k
views
What is the difference between vst and rlog to perform PCA ?
rlog PCA vsd
updated 11 months ago by 82k • written 11 months ago by ▴ 160
4
votes
5
replies
2.0k
views
Whole blood single cell RNA-seq dataset?
RNA-Seq scRNA-Seq whole blood single cell
12 months ago by predeus ★ 1.9k
4
votes
4
replies
360
views
Average expression of a sample in single-cell data
single-cell rna-seq
24 days ago by newuser2024 • 0
4
votes
5
replies
1.1k
views
STAR mapping - regarding output files content
STAR RNA-seq mapping
updated 8 months ago by ▴ 900 • written 8 months ago by • 0
1,000 results • Page 3 of 20
Recent Votes
A: How to process (seems) Agilent microarrry data?
Comment: genome assembly records not present in assembly_summary.txt
Answer: genome assembly records not present in assembly_summary.txt
Answer: PCA plot (Suggestions Needed)
Comment: PCA plot (Suggestions Needed)
Comment: PCA plot (Suggestions Needed)
Comment: PCA plot (Suggestions Needed)
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Recent Replies
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…
Comment: ScRNA data question by starswillfade ▴ 10
I just thought it was weird that considering each dot is a cell their expressions were all on a single line instead of being spread out lik…
Comment: ScRNA data question by starswillfade ▴ 10
![enter image description here][1] I am already using Seurat V5 I think. I am using SCTransform as it was recommended by the seurat page. I…
Answer: genome assembly records not present in assembly_summary.txt by GenoMax 141k
Can you clarify what `metainfo` you are referring to? The accession that you refer to does exist in [**GenBank assembly_summary file**][1…
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