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121,395 results • Page 588 of 2428
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0
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2
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2.5k
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Linux command to delete empty fastq.gz files
linux fastq gz
updated 3.9 years ago by 21k • written 3.9 years ago by • 0
0
votes
0
replies
966
views
VCF to 23 and Me format and changing ensamble reference help needed for underestanding VCF
23andMe VCF
3.9 years ago by aliciabasilo.ab • 0
0
votes
0
replies
775
views
Download COG Database
database COG
3.9 years ago by gaurav.iari • 0
3
votes
2
replies
1.9k
views
How to interpret bimodal distribution of GC-content for RNAseq and can it be remedied ?
RNA-Seq GCcontent FastQC RNAseq
updated 3.9 years ago by 152k • written 3.9 years ago by ▴ 220
5
votes
3
replies
2.0k
views
AnnotationHub::mapIds() cannot find existing ENSG (GEO supplemental data cross-referenced with ensembl.org)
ensg annotationhub mapping
3.9 years ago by mk ▴ 310
1
vote
5
replies
2.1k
views
De novo genome assembly
De novo Assembly Genome Minimap2 Mother
updated 3.9 years ago by 152k • written 3.9 years ago by • 0
1
vote
0
replies
1.1k
views
hisat2 compatibility for long read
Long-read hisat2
updated 24 months ago by 45k • written 3.9 years ago by ▴ 20
2
votes
1
reply
3.1k
views
illumina adapter specifying and removing using fastp
adapter index illumina fastp fastq
updated 3.9 years ago by 152k • written 3.9 years ago by ▴ 820
0
votes
2
replies
1.2k
views
Extremely low number of variants in VCF file after filtering MIN(FORMAT/DP)>10
bcftools snp vcf calling
updated 3.9 years ago by 21k • written 3.9 years ago by ▴ 80
0
votes
1
reply
2.0k
views
extract list of SNPs from multiple chr{1:22}.bgen files using plink2
subset of extract maf SNPs cutoff plink2
updated 3.9 years ago by 11k • written 3.9 years ago by ▴ 10
1
vote
3
replies
2.4k
views
formatting error: Calculate LD matrix from bgen file
plink ld_matrix
updated 12 months ago by 45k • written 3.9 years ago by ▴ 160
0
votes
0
replies
660
views
Mixed model analysis using lme4
mixed-model fixed-effect lme4 random-effect lmer
updated 9 months ago by 45k • written 3.9 years ago by ▴ 20
12
votes
8
replies
4.0k
views
7 follow
Highly used R packages with no Python equivalent
package python r software
updated 3.9 years ago by 11k • written 3.9 years ago by • 0
1
vote
2
replies
3.5k
views
install ensembl-vep
ensembl-vep install
3.8 years ago by yueli7 ▴ 250
2
votes
3
replies
1.3k
views
How to separate sub-families from transposons sequence based fasta files?
fasta transposons
updated 2.2 years ago by 45k • written 3.9 years ago by • 0
2
votes
1
reply
974
views
calculating fold change from dataframe
fold frame change data
updated 3.9 years ago by 88k • written 3.9 years ago by • 0
1
vote
4
replies
1.3k
views
Variant calling from 5 MB regions coming from contrasting cultivars
calling alignment variant
3.9 years ago by VenGeno ▴ 100
0
votes
0
replies
517
views
variant filtration with gene names or position
variant-filtration
3.9 years ago by ziziqolo ▴ 10
0
votes
1
reply
778
views
How does find the sequence of each oligonucleotide in microarray probe?
Affymetrics technology probe microarray
updated 3.9 years ago by 21k • written 3.9 years ago by ▴ 170
2
votes
3
replies
2.5k
views
How to subset vcf by sample and write?
bcftools vcf
updated 3.9 years ago by ▴ 480 • written 3.9 years ago by ▴ 50
0
votes
4
replies
2.2k
views
Can RNA-Seq be used for TMB calculation?
RNA-Seq tmb
updated 3.9 years ago by 89k • written 4.6 years ago by ▴ 10
0
votes
5
replies
8.2k
views
bcftools consensus still returns "Could not parse the header" error
bcftools samtools
3.9 years ago by shpak.max ▴ 60
1
vote
1
reply
1.5k
views
Detecting and masking repeats with EDTA: Low threshold vs complete masking
repeat masker. annotation genome EDTA
updated 3.9 years ago by ▴ 30 • written 3.9 years ago by • 0
7
votes
5
replies
1.6k
views
Why does Txdb transcript length not always match to transcript end-start position?
biomart transcript Txdb length transcription
updated 3.9 years ago by 21k • written 3.9 years ago by ▴ 20
0
votes
5
replies
2.7k
views
printing volcano plot
bioinfokit python gene_expression volcano_plot
updated 3.9 years ago by 45k • written 3.9 years ago by • 0
1
vote
0
replies
453
views
Myeloma Data Search
myeloma
updated 2.5 years ago by 45k • written 3.9 years ago by ▴ 140
2
votes
4
replies
5.1k
views
Interpreting bcftools isec output
bcftools isec intersection vcf
updated 3.5 years ago by 45k • written 3.9 years ago by ▴ 30
5
votes
4
replies
2.8k
views
How do we process Kallisto output (continuous real values) for DESEQ2 analysis (which strictly require discrete count values)?
read-counts DESEQ2 differential-gene-expression kallisto
updated 14 months ago by 45k • written 3.9 years ago by ▴ 180
0
votes
0
replies
922
views
Job: Product Manager for Online Bioinformatics Resources for Online Bioinformatics Resources
Resources Product-Manager
updated 2.3 years ago by 45k • written 3.9 years ago by ▴ 90
0
votes
2
replies
2.3k
views
[pysam] How to find both both primary and supplementary read？
NGS pysam bam python SAM
3.9 years ago by octpus616 ▴ 120
1
vote
2
replies
1.4k
views
question about Mutation Annotation Format (MAF) variant classifications
annotation ICGC MAF R
3.9 years ago by Charles Murtaugh ▴ 50
0
votes
1
reply
713
views
Cytogenetics Database
database ISCN Cytogenetics
3.9 years ago by Jng • 0
0
votes
3
replies
1.4k
views
KCCG /ClinSV issue with hg38
variation human genome wgs
3.9 years ago by Ishak ▴ 20
13
votes
15
replies
12k
views
6 follow
Where To Find Annotation File For Agilent Microarray?
annotation
updated 3.9 years ago by ▴ 20 • written 11.9 years ago by ★ 1.1k
0
votes
0
replies
601
views
Find causal mutation for a special trait in one population
Detecting SV SNP
3.9 years ago by dominik.lagler ▴ 30
0
votes
0
replies
670
views
Genbank submission problem
tbl genbank gbff submission
3.9 years ago by hs • 0
0
votes
1
reply
1.1k
views
errors installing HTSeq
HTSeq RNAseq
updated 3.9 years ago by 152k • written 3.9 years ago by • 0
2
votes
3
replies
1.1k
views
Genotyping variants from BAM (human)
genotyping
updated 3.9 years ago by 152k • written 3.9 years ago by ★ 3.0k
0
votes
0
replies
533
views
Getting the average of pdb structure from only one trajectory
PBD Trajectory
updated 3.9 years ago by 55k • written 3.9 years ago by • 0
3
votes
1
reply
3.8k
views
Issues with enricher() function from clusterProfiler
clusterProfiler enrichment
updated 3.9 years ago by ★ 2.6k • written 4.4 years ago by ▴ 10
0
votes
13
replies
3.2k
views
Default CNV call thresholds for haplotype chromosome s
haplotype cnvkit mal calling cnv
updated 3.8 years ago by ★ 3.0k • written 3.9 years ago by ▴ 40
0
votes
0
replies
877
views
Job: PostDoc in Bioinformatics / Machine Learning (Luxembourg, Europe)
PostDoc machine-learning
updated 2.3 years ago by 45k • written 3.9 years ago by ▴ 130
4
votes
4
replies
2.6k
views
How do I export a KaryoploteR plot or insert it into a grid/lattice? Can I assign a KaryoploteR plot to a variable?
karyoploteR grid ideograms
updated 3.9 years ago by ▴ 120 • written 3.9 years ago by ▴ 20
2
votes
3
replies
1.6k
views
Cannot compile Lumpy-SV.
structural KCCG ClinSV variation
3.9 years ago by Ishak ▴ 20
6
votes
5
replies
1.7k
views
How to Append numbers on ALL headers in FASTA (e.g., >gene#1)?
FASTA perl Python
updated 3.9 years ago by 21k • written 3.9 years ago by ▴ 10
0
votes
2
replies
1.3k
views
How do you perform in silico PCR ?
taxonomy PCR NCBI
updated 3.9 years ago by ▴ 840 • written 3.9 years ago by • 0
4
votes
2
replies
2.2k
views
convert GenBank formatted sequence file to FASTA format
fasta python genback
updated 3.8 years ago by 45k • written 3.9 years ago by ▴ 20
6
votes
6
replies
5.1k
views
SRA-tools fasterq-dump and cellranger issues
cellranger
updated 2.7 years ago by ▴ 20 • written 3.9 years ago by ▴ 10
0
votes
4
replies
1.7k
views
Functional enrichment and visualization of metatranscriptomics data
clusterProfiler
3.9 years ago by shail.nair05 ▴ 20
1
vote
0
replies
614
views
question about integrating snRNA seq data from different batch and different experimental conditions
Seurat batch integrate
3.9 years ago by Wonjae ▴ 10
121,395 results • Page 588 of 2428
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Answer: Should I perform integration to correct batch effects?
Should I perform integration to correct batch effects?
Answer: Batch correction in TNBC epithelial cells
Answer: When should I NOT apply batch correction for my single-cell RNAseq data?
Answer: Should I perform integration to correct batch effects?
Answer: Batch correction in TNBC epithelial cells
Comment: convert raw counts to TPM
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Recent Replies
Comment: Single-cell RNA Sequencing - transcript abundance estimation using Alevin-Fry by Rob 7.1k
The main issue is that there will be an inherent lack of information (due to the aforementioned 3' bias) in tagged-end data. Nonetheless, …
Comment: Y-axis break in Volcano Plot by antonioggsousa 3.3k
I am not familiar with the package `EnhancedVolcano`, but based on your code, should not you be able to change the y-axis limits through th…
Answer: Clarification of options --keep-dup: all vs. -f FRAG in MACS3 by ATpoint 88k
As per the manual, `FRAG` is specific for scATAC-seq while the other option is generic.
Answer: Should I perform integration to correct batch effects? by antonioggsousa 3.3k
Hi, Please check my previous answer to a similar post/question on this forum: [When should I NOT apply batch correction for my single-cel…
Answer: Batch correction in TNBC epithelial cells by ATpoint 88k
> (1) Is my pipeline correct? Especially re-applying the harmony to the sub-setted the TNBC epithelial cells. You **can** do that. No prob…
Comment: Different comparisons in RNASeq Analysis by mbyvcm ▴ 460
My suggestion is that you consider performing what is commonly referred to as a "delta-delta" contrast. You should be able to find plenty o…
Comment: mgl tool index error by Mahesh • 0
no i am simply drag and drop my pdbqt file in GUI
Answer: Best way to install R packages on an HPC? by Charles Plessy ★ 2.9k
At my workplace I created a Singularity image that has most of the C/C++ libraries installed, and R's library path pointing to an image-spe…
Comment: Best way to install R packages on an HPC? by cfos4698 ★ 1.1k
FWIW, I've recently still been running into environment solving issues with conda (even with the incorporated libmamba changes) that mamba …
Comment: How to interpret genomescope to help remove duplicates by mohamadelian1996 • 0
Thank you for helping me out. Other related species have genomes ranging between 400 and 700 Mb so the length given here by genomescope see…
Comment: How to interpret genomescope to help remove duplicates by GenoMax 152k
What is the expected genome size and ploidy for this organism? Can you post the busco results?
Comment: Is it valid to stack brightfield and fluorescence channels in a CNN input? by LChart 5.0k
Not a real answer, but it should be pointed out that the only way to learn contrastive filters across modalities (i.e., fluorescence-only e…
Answer: Is it valid to stack brightfield and fluorescence channels in a CNN input? by Mensur Dlakic ★ 29k
I think this is a borderline bioinformatics question, but I'll still attempt to answer. You won't break the computer by merging all three …
Comment: mgl tool index error by GenoMax 152k
Are you using command line or some sort of GUI? Post the full command if you are doing this on the command line.
Comment: Snakemake Module Error: string indices must be integers by Jesse ▴ 870
But wait, is the idea with modules that you supply a preloaded config for that module, or that you supply a *path* to a separate config, li…
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