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121,992 results • Page 261 of 2440
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1.6k
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Prefecth-orig and fasterq-dump not working when downloading SRA files (v3.0.5)
Windows SRAtoolkit sra
updated 2.4 years ago by 45k • written 2.4 years ago by • 0
5
votes
4
replies
2.6k
views
Protein fold topology search web-server
topology structure protein
updated 2.4 years ago by ★ 2.1k • written 2.4 years ago by ▴ 110
8
votes
8
replies
6.6k
views
How To Control Wgsim Base Qualities?
fastq gatk
updated 2.4 years ago by • 0 • written 13.8 years ago by ★ 1.5k
0
votes
2
replies
2.3k
views
cutadapt: how to trim adapter dimers?
cutadapt small-RNAseq adapters
updated 2.4 years ago by ▴ 880 • written 2.4 years ago by • 0
4
votes
5
replies
2.6k
views
How come on T2T human genome assembly the PAR regions of chrY are bigger than the corresponding regions on chrX?
genome assembly T2T
updated 2.4 years ago by 4.8k • written 2.4 years ago by ▴ 240
0
votes
1
reply
1.1k
views
WES variant calling with DNBSEQ-T7 - technical quality assessment
WES DNA-seq GATK variant-calling mutect2
updated 2.4 years ago by 8.0k • written 2.4 years ago by ▴ 170
0
votes
0
replies
682
views
GC content of WES cohort
WES FASTQC GC-content
updated 2.4 years ago by 45k • written 2.4 years ago by ▴ 250
0
votes
0
replies
750
views
Creating CIBERSORTx signature matrix
CIBERSORTx
2.4 years ago by FrankStarling ▴ 60
0
votes
1
reply
653
views
Can I consider these values as differentially expressed?
DESeq2
updated 2.4 years ago by 103k • written 2.4 years ago by • 0
0
votes
0
replies
738
views
Will this method for genomic population structure analysis with VCF file help good for my work?
population-genomics VCF PCA
updated 2.4 years ago by 45k • written 2.4 years ago by • 0
6
votes
7
replies
2.0k
views
extracting data from single end aligned bam file - chromosome, strand, start and stop from cigar
bam
updated 2.4 years ago by 103k • written 2.4 years ago by ▴ 80
0
votes
0
replies
621
views
Generating TSS heatmap using methylation data
wgbs r tss methylation heatmap
2.4 years ago by Minsun • 0
3
votes
4
replies
985
views
Mapping to single sequence
NGS Sequencing Mapping
updated 2.4 years ago by 154k • written 2.4 years ago by • 0
0
votes
1
reply
772
views
Predict species from DNA sequences
Species Classification ML
updated 2.4 years ago by ★ 4.0k • written 2.4 years ago by • 0
0
votes
1
reply
681
views
CRISPR-DAV: How to make a reference genome file
crisprdav indeldetection ngs knockout crispr
updated 2.4 years ago by 154k • written 2.4 years ago by • 0
0
votes
0
replies
534
views
pseudo-bulk
scRNAseq DE
updated 2.4 years ago by 45k • written 2.4 years ago by ▴ 10
0
votes
2
replies
1.0k
views
Change VCF File Reference Genome to a Local .FA File
VCF fasta
updated 2.4 years ago by 48k • written 2.4 years ago by • 0
0
votes
0
replies
452
views
How to use a design matrix with two control levels in DESeq2
design_matrix contrast DESeq2
2.4 years ago by Pac314 ▴ 10
0
votes
0
replies
578
views
Variants in Clinvar which are not linked to dbSNP
RS dbSNP Clinvar
2.4 years ago by Manuel • 0
1
vote
2
replies
3.6k
views
Visualize smooth ChIP peaks with Homer makeUCSCfile
homer ucsc ChIP-Seq
updated 2.4 years ago by • 0 • written 8.3 years ago by ▴ 90
3
votes
3
replies
2.4k
views
MULTIQC problem
MULTIQC
updated 2.3 years ago by 45k • written 2.4 years ago by ▴ 10
5
votes
6
replies
2.3k
views
How to efficiently/quickly merge ~500k vcfs?
bcftools vcf variant-calling
updated 2.4 years ago by 23k • written 2.4 years ago by ▴ 20
1
vote
8
replies
2.7k
views
BLAST Database error: BLASTDB alias file creation failed. Some referenced files may be missing.
blastdb blast
updated 2.4 years ago by 45k • written 2.4 years ago by ▴ 120
0
votes
2
replies
974
views
Using a transcriptome from Trinity in Phyluce
Phyluce transcriptome RNA trinity
2.4 years ago by luzglongoria ▴ 50
1
vote
6
replies
1.6k
views
DESeq2
heatmap R DESeq2
2.4 years ago by Nelo ▴ 20
0
votes
0
replies
388
views
runs of homozygosity
H R
updated 2.4 years ago by 154k • written 2.4 years ago by • 0
1
vote
2
replies
1.6k
views
How to find coordinates of TSS from 5pUTR and TTS from 3pUTR in transcriptome/ mRNA ?
coordinates
11 months ago by isha.lily20 ▴ 10
0
votes
2
replies
852
views
How do I figure out what splicing variant is expressed in certain tissue?
rnaseq rna-seq sequencing NGS splicing
2.4 years ago by James • 0
0
votes
0
replies
707
views
News: PROGRAMMING IN R : MOVING FROM BEGINNER TO ADVANCED
Programming Training R
2.4 years ago by Physalia-courses ★ 2.6k
121
votes
33
replies
44k
views
24 follow
Forum: Where To Look For Quality Bioinformatics Short Courses And Workshops?
Courses
updated 2.4 years ago by ★ 2.6k • written 12.1 years ago by 11k
3
votes
6
replies
1.4k
views
How to interpret plot from igv_session.xml file
ATAC
15 months ago by Chris ▴ 360
1
vote
2
replies
1.1k
views
Bowtie2 alignment on metagenomics - sum same sequence
metagenomics Bowtie2
updated 2.4 years ago by ★ 2.4k • written 2.4 years ago by • 0
2
votes
2
replies
1.4k
views
Question on removing duplicates with ATAC-Seq and ChIP-Seq
clumpify chip-seq atac-seq bbmap
2.4 years ago by tamu.anand ▴ 30
1
vote
1
reply
933
views
How do you go about grabbing proper genotyping information from dbSNP using entrez API?
ncbi R python dbsnp entrez
updated 2.4 years ago by ★ 2.5k • written 2.4 years ago by ▴ 20
0
votes
0
replies
608
views
sPLS-DA and LASSO regression for feature selection against one dependent variable
sPLS-DA LASSO regression statistics
2.4 years ago by Jonathan Yoou ▴ 70
1
vote
1
reply
832
views
Unexpected break in site frequency spectrum pattern
frequency sfs Stacks site spectrum populations
2.4 years ago by S ▴ 10
0
votes
1
reply
1.2k
views
GSEA with duplicate sample
rna-seq GSEA
updated 2.4 years ago by ★ 1.9k • written 2.4 years ago by ▴ 60
0
votes
0
replies
445
views
cerna network
cerna
2.4 years ago by ali • 0
0
votes
0
replies
477
views
Downloading a selected list of methylation probes from cBioportal
methylation datamining probes cbioportal rbioconductor
2.4 years ago by bouchra.tawk • 0
0
votes
2
replies
812
views
Loop through file to assign alphabets to genefeatures for the read intersects
bedintersect python awk
2.4 years ago by L_bioinfo • 0
4
votes
3
replies
1.6k
views
Loop through comma separated values and find match from another file
awk
updated 2.4 years ago by 166k • written 2.4 years ago by • 0
0
votes
1
reply
1.4k
views
How to filter the BAM file using barcode list produced by 10x pipelines?
list barcode
updated 2.4 years ago by 154k • written 2.8 years ago by ▴ 30
0
votes
0
replies
845
views
Analyse UMI using picard's ExtractIlluminaBarcodes & IlluminaBasecallsToSam with 2 or 4 lanes
picard umi
2.4 years ago by User000 ▴ 750
0
votes
0
replies
939
views
How to match ellipse and point color in PCA plot (fviz_pca_biplot)?
ellipse biplot fviz_pca_biplot PCA geometry
2.4 years ago by Doralicia • 0
103
votes
42
replies
35k
views
34 follow
Forum: List of cloud genomics companies
cloud-genomics
updated 5 days ago by 23k • written 11.9 years ago by ★ 3.6k
1
vote
2
replies
856
views
Should I use mean to show variations among different studies in meta analysis
meta-analysis R
2.4 years ago by rishav513 ▴ 30
0
votes
0
replies
501
views
how to retrieve the chunk of every chromosome from a vcf file
haplotyping varaints
2.4 years ago by rj.rezwan ▴ 20
2
votes
3
replies
1.0k
views
What's your recommended length and depth for my RNA-seq experiment
RNA-seq
updated 2.4 years ago by ★ 1.7k • written 2.4 years ago by ▴ 10
6
votes
3
replies
1.7k
views
Issue about generating EMBL Flat file for ENA submission
EMBL ENA EMBLmyGFF3
updated 2.2 years ago by ▴ 20 • written 2.4 years ago by ▴ 50
0
votes
0
replies
739
views
Plink1.9, keeping order of updated samples IDs
SNPs samples Plink
2.4 years ago by AMARU • 0
121,992 results • Page 261 of 2440
Recent Votes
A: Trimmomatic Error: Unable to detect quality encoding
A: Trimmomatic Error: Unable to detect quality encoding
Answer: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions
Comment: Tools to simulate Illumina short read sequences and ONT long reads with a refere
Answer: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions
Answer: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions
Answer: TMM-Normalization
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Recent Replies
Answer: SNP calling ONT sequenced files by cfos4698 ★ 1.2k
My personal preference is using [clair3][1]. I'm unsure if CLC didn't work because your compute resources are too limited, or if there are …
Comment: HIV NL4-3 transcriptome fasta by Ales ▴ 50
Hi, Wanted to update here that full transcriptome annotations for thousands of hiv genomes (including NL4-3) are now available at https://…
Answer: HIV NL4-3 transcriptome fasta by Ales ▴ 50
You can get full transcriptome annotation for the NL4-3 genomes: https://ccb.jhu.edu/HIV_Atlas/11676/AF324493.2 . Note the accession ID tho…
Answer: Doubt on docking by Mensur Dlakic ★ 30k
I think you are wrongly assuming that we can help you with this without knowing what is the protein of interest. A general answer is that …
Answer: Difficulty running FoldX in linux by Mensur Dlakic ★ 30k
The post looks much better now, so you did something. The preview here works fine. It simply can't be that the preview for your original po…
Comment: GUI commercial software for 10x single cell gene expression analysis by GenoMax 154k
Black box software has its cons but in instances like what OP needs that may be the only viable option. Their use limits reproducibility as…
Comment: downloading raw bam files from pacbio sequencer by GenoMax 154k
Have you checked : https://www.pacb.com/connect/datasets/
Comment: TMM-Normalization by kalavattam ▴ 380
No, but a modified version of TMM does: “GeTMM.” See the paper [here](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-0…
Comment: Difficulty running FoldX in linux by strayeroliver • 0
Responding to your answer. - I spent a lot of time formatting it just right, using the ``` methodology you mentioned. It looks very good o…
Comment: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions by Phil Ewels ★ 1.5k
Found the docs: https://www.nextflow.io/docs/latest/process.html#multiple-input-files | Arity | Name pattern | Staged file names | |---|--…
Comment: Dorado in PowerShell on Windows by jared.andrews07 ★ 19k
No more than running it on native Linux (as that's what WSL is at this point).
Answer: SNP calling ONT sequenced files by colindaven 8.0k
The quality of (modern, SUP basecalled, but certainly not fast basecalled) ONT sequences should be fine, especially for bacterial SNP call…
Comment: SNP calling ONT sequenced files by GenoMax 154k
What is the median length of raw reads and how many do you have? Has the data been basecalled with "high" or "super" accuracy? > I have …
Comment: Tools to simulate Illumina short read sequences and ONT long reads with a refere by GenoMax 154k
This question is about simulating reads and not read mapping.
Comment: GUI commercial software for 10x single cell gene expression analysis by yura.grabovska ▴ 830
I have fun memories of month-long discussions with Illumina support about their GenomeStudio methylation module asking them to provide info…
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