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122,013 results • Page 299 of 2441
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2
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1
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1.8k
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Axiom PMRA cel files to VCF format
PMRA CEL Intensities Axiom VCF
updated 2.7 years ago by ▴ 630 • written 2.7 years ago by • 0
0
votes
0
replies
597
views
Next generation sequencing variant calling pipeline
WGS Targeted WES Sequencing
updated 2.7 years ago by 89k • written 2.7 years ago by ▴ 260
0
votes
3
replies
1.0k
views
Unable to validate biomarkers obtained from single-cell RNA-seq data
biomarkers single-cell Seurat
updated 2.7 years ago by 89k • written 2.7 years ago by ▴ 240
1
vote
4
replies
1.4k
views
Clarification on the usage of pangenomeHaplotypeMethod/pathHaplotypeMethod
phg
2.6 years ago by twrl8 • 0
0
votes
1
reply
639
views
How to count the total read mapped to each chromosome using sam/bam after alignment?
bam sam reads mapped
2.7 years ago by Diego ▴ 110
0
votes
2
replies
905
views
Recommendations for API/Flat file DB describing physical and biological properties of human proteins
protein cheminformatics informatics
updated 2.7 years ago by ★ 2.4k • written 2.7 years ago by ▴ 60
0
votes
0
replies
844
views
Determining and removing outlier by eigenvectors generated by PLINK
outliers eigenvectors PCA vcf PLINK
2.7 years ago by Arda • 0
3
votes
2
replies
1.6k
views
BBMap/sh/repair.sh not finding pairs
BBMap fastq repair paired-end repair.sh
updated 2.7 years ago by 5.1k • written 2.7 years ago by ▴ 10
7
votes
7
replies
4.0k
views
Extracting gapped sequences from Bio.Align.PairwiseAligner
pairwise2 PairwiseAligner BioPython
updated 2.7 years ago by 22k • written 2.7 years ago by ▴ 50
0
votes
0
replies
650
views
News: course - Next steps in applied Bayesian regression modeling
Statistics RegressionModeling Bayesian R
2.7 years ago by Physalia-courses ★ 2.7k
5
votes
1
reply
2.1k
views
Picard MarkDuplicates and EstimateLibraryComplexity - incongruency in duplicates percentage
picard markduplicates
2.7 years ago by ipediez93 ▴ 40
0
votes
0
replies
455
views
SV tool recommandation for detecting 50bp> deletion sequence
structural-variants NGS WGS
updated 2.6 years ago by 45k • written 2.7 years ago by • 0
0
votes
1
reply
1.1k
views
[E::idx_find_and_load] warning in htseq-count
idx_find_and_load htseq-count
updated 2.6 years ago by ★ 3.0k • written 2.7 years ago by ▴ 10
2
votes
2
replies
855
views
Using DESeq2 to data normalization
DESeq2
2.5 years ago by Hello • 0
0
votes
0
replies
1.9k
views
harmony output
Harmony R
2.7 years ago by Andy ▴ 120
0
votes
3
replies
1.4k
views
How many basepairs are genes padded by in WES?
NGS sequencing WES exome
updated 2.7 years ago by ▴ 290 • written 2.7 years ago by ▴ 90
0
votes
1
reply
1.4k
views
interpreting voom mean variance plots with large BCV and faint kink
filtering differential-expression voom gene
updated 2.7 years ago by ★ 8.3k • written 2.7 years ago by ▴ 40
0
votes
1
reply
1.3k
views
MAGeCK mle returns all genes as essential
CRISPR MAGeCK
updated 2.7 years ago by 89k • written 2.7 years ago by • 0
1
vote
0
replies
962
views
What are the differences between GSVA and ssGSEA (in layman's term)?
ssGSEA GSVA GSEA
2.7 years ago by cwwong13 ▴ 40
2
votes
3
replies
2.1k
views
How to fix "Contig chrKI270728.1 not present in the sequence dictionary " error
NGS Sequencing BQSR VCF
updated 2.7 years ago by 45k • written 2.7 years ago by ▴ 60
3
votes
2
replies
3.3k
views
Downloading "dbsnp 146.hg38.vcf.gz" file for BQSR
NGS dbsnp WES BQSR
2.7 years ago by Yoosef ▴ 60
1
vote
4
replies
2.6k
views
From VCF to BEAGLE format with multiple chromosomes
vcf vcftools beagle gvcf
2.4 years ago by Begonia_pavonina ▴ 210
0
votes
1
reply
2.2k
views
Assigning multiple identities to seurat metadata
single-cell Seurat scRNA-seq
updated 2.7 years ago by 45k • written 2.7 years ago by • 0
0
votes
0
replies
517
views
Anyone has experience with using methylCC/Bioconductor to obtain cell composition (blood) for whole-genome bisulfite sequencing (WGBS)?
deconvolution WGBS methylCC
2.7 years ago by Lalaland ▴ 40
5
votes
12
replies
2.5k
views
Data from an experiment
single-cell
updated 2.7 years ago by 154k • written 2.7 years ago by ▴ 360
1
vote
1
reply
1.2k
views
Error while running survival analysis ?
KM OS plot RNA-Seq
updated 2.7 years ago by ▴ 370 • written 2.7 years ago by ▴ 60
4
votes
10
replies
1.7k
views
Extract unmapped reads OR reads covering chromosome 6 from a bam file?
fastq bam samtools picard
2.7 years ago by bioinf_sci ▴ 20
1
vote
1
reply
963
views
invalid --hwe parameter sequence error when doing QC
QC
updated 2.7 years ago by 11k • written 2.7 years ago by ▴ 10
1
vote
1
reply
667
views
bcftools annotate added most rs IDs, but not all.
bcftools
updated 2.3 years ago by 45k • written 2.7 years ago by • 0
2
votes
3
replies
2.1k
views
Converting multiple files from Clustal to MEGA format
alignment clustalw mega
2.7 years ago by alexander.brg • 0
2
votes
2
replies
1.4k
views
How to generate "dummy"/"fake" VCFs for testing software?
vcf
updated 2.7 years ago by 166k • written 2.7 years ago by ▴ 70
0
votes
2
replies
800
views
Pearson correlation coefficients of histone modifications at specific region
histone-modification chip-seq
updated 2.7 years ago by 45k • written 2.7 years ago by ▴ 30
1
vote
4
replies
813
views
FASTQC RESULTS
fastqc
2.7 years ago by mshayat • 0
14
votes
15
replies
7.4k
views
K-mer sequencing vs sequence-alignment
short-reads next-gen alignment k-mer
updated 2.7 years ago by 45k • written 4.7 years ago by ▴ 40
3
votes
3
replies
1.0k
views
Is there a programatic way of checking if a cyanobacteiral ITS region motif is accurate?
folding motif secondary cyanobacteria ITS
updated 2.7 years ago by ★ 30k • written 2.7 years ago by ▴ 20
2
votes
6
replies
2.4k
views
Design and Contrast Matrix in Limma Analysis
R
updated 2.7 years ago by 5.1k • written 2.7 years ago by ▴ 140
0
votes
0
replies
664
views
How to handle KEGG orthologous IDs involved multiple pathways
KEGG annotation metagenome functional gene
2.7 years ago by young_bioinformatician ▴ 240
1
vote
2
replies
1.0k
views
use cutadapt to trim bases at begaining of each reads
trimming adapter bases cutadapt
2.7 years ago by Qianjiang(QJ) Hu ▴ 10
1
vote
5
replies
1.6k
views
GATK 4.3 configuration
cofig GATK
2.7 years ago by wonde2000 • 0
0
votes
0
replies
687
views
How to format matrix with negative values for NMF in R
nmf R matrix
2.7 years ago by yura.grabovska ▴ 850
3
votes
3
replies
3.8k
views
python function to kmer with windown size
python kmer biopython fasta
updated 2.7 years ago by • 0 • written 5.8 years ago by ▴ 280
0
votes
1
reply
1.8k
views
Kraken report or mph report to phyloseq object
metaphlan kraken phyloseq
updated 2.7 years ago by ▴ 10 • written 3.9 years ago by ▴ 50
0
votes
5
replies
2.1k
views
urllib.error.HTTPError: HTTP Error 400: Bad Request with biopython Entrez
ncbi bioython entrez
updated 2.7 years ago by 154k • written 2.7 years ago by • 0
0
votes
0
replies
578
views
Much less peaks compared to other replicates
replicates ATAC-seq
2.7 years ago by zau saa ▴ 150
0
votes
4
replies
1.3k
views
What to do if hundreds or genes have no functional domain!
functional gene annotation
2.7 years ago by ahmadjoyyia ▴ 30
0
votes
0
replies
768
views
What is the different bewteen ucsc simple repeat and tandem repeat
reference USCS annotation hg38
2.7 years ago by octpus616 ▴ 120
1
vote
1
reply
757
views
edgeR error
EdgeR R DEG
updated 2.6 years ago by 45k • written 2.7 years ago by • 0
0
votes
1
reply
763
views
How do I edit chromosome names or delete some chromosomes in assembly (FASTA) and annotation (GFF/GTF) file?
chromosome
updated 2.7 years ago by ★ 19k • written 2.7 years ago by • 0
1
vote
3
replies
1.1k
views
Error Accessing Values in Snakemake Config File
Snakemake
updated 2.7 years ago by ▴ 120 • written 2.7 years ago by • 0
4
votes
4
replies
2.0k
views
Do I need to adjust the pvalue if I am only going to test one gene from omics data containing many genes?
pvalue Omics RNAseq
2.7 years ago by cwwong13 ▴ 40
122,013 results • Page 299 of 2441
Recent Votes
A: Bam And Indexed Bam Files
Answer: How to create a phylogenetic tree from 30 VCF files
Comment: Reading AD and other genotype information from the VCF file
Answer: 1 vs 1 DEG analysis in scrna seq data
Comment: installation of package ‘DESeq2’ had non-zero exit status
Answer: Recommendations for 200 SNP markers genotyping
Comment: Reasonable number of SNPs in a bacterial genome.
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Answer: 1 vs 1 DEG analysis in scrna seq data by ATpoint 89k
The only option you have is to treat every single cell as a replicate. That has the obvious downside that any effect can be a donor-unique …
Answer: GUI commercial software for 10x single cell gene expression analysis by firestar ★ 1.7k
An open-source option: [kana](https://www.kanaverse.org/kana/).
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by Edward • 0
Yes, we plan to make English the primary language of the Brave UI.
Comment: Reasonable number of SNPs in a bacterial genome. by michael.ante ★ 4.0k
If your bacterial species is a (human) pathogen, you might want to check outbreak analysis papers of that species. In general, you find t…
Comment: hisat2 error-Paired end reads not equal or lack of RAM/disk space? by lieven.sterck 16k
ok, missed that ... in any case that should not happen indeed. How did you determine that the files are not equal? I can indeed also see t…
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by Ram 45k
Do you have a plan to make an English version of the UI?
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by Edward • 0
This can visualize the parameters of the generated workflow, software, and scripts, and manage the docker process of the script, software, …
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by ATpoint 89k
Can you summarize in one sentence what the use case is? Is this a workflow manager?
Comment: Pseudogene - scarce info by ATpoint 89k
This reminds me strongly on my "masters" courses (doesn't deserve that name tbf). "Here is some poorly-described project with little to no …
Answer: scVI vs Harmony, which is better for cell type based clustering in brain tissue? by ATpoint 89k
There is no "better" is my experience. It always depends on the dataset. Try both and integrate your biological knowledge to decide which m…
Comment: DESeq2 on metagenome KO counts by Aleksandra ▴ 190
I just wrote that I misunderstood your initial question.
Comment: DESeq2 on metagenome KO counts by Aleksandra ▴ 190
What exactly did I not get?
Comment: Interpreting genomic features distribution for CUT&RUN peaks by rfran010 ★ 1.7k
If I understand correctly, you see increased signal at TSS sites compared to control (taller peaks in browser). However, 92% of the 450 siS…
Comment: combine VCF from diploid reference/haplotypes for the same sample by cmdcolin ★ 4.3k
this question is a little similar to your previous question (https://www.biostars.org/p/9614638/). just as added info, here is a tool calle…
Comment: hisat2 error-Paired end reads not equal or lack of RAM/disk space? by aj123 ▴ 130
As mentioned above, I just got the raw fastq files from the ftp site listed.
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