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121,990 results • Page 255 of 2440
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3
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5
replies
3.5k
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Uniprot API access to download .pdb files
PDB API Python Uniprot
2.4 years ago by BioGrad321 • 0
2
votes
1
reply
791
views
Analytical criteria to say a transcript is expressed in single-cell
counts scRNA-seq single-cell expression-matrix
updated 2.4 years ago by 45k • written 2.4 years ago by ▴ 80
1
vote
2
replies
1.1k
views
highlight regions in a dot-plot?
figure dotplot alignment synteny
2.4 years ago by Buffo ★ 2.4k
4
votes
8
replies
3.3k
views
Obtaining the AF and DP values for variants in a VCF
DP mutect2 SNP vcf AF
updated 2.4 years ago by 45k • written 2.4 years ago by ▴ 40
0
votes
2
replies
1.1k
views
Samtools index and sambamba-depth error?
linux samtools sambamba
updated 2.3 years ago by 45k • written 2.4 years ago by ▴ 20
0
votes
3
replies
1.3k
views
How to extract out gene specific reads from concatenated fastq file
fastq gene-specific RNA-seq nanopore
2.4 years ago by Mo ▴ 50
0
votes
3
replies
1.4k
views
PLINK not converting entire vcf to bed file
vcf plink genome1000 bed
2.4 years ago by ethan.kreuzer • 0
6
votes
17
replies
3.6k
views
MacOS Quicklook plugin for gtf and gff3 files?
gtf gff3 MacOS
updated 2.4 years ago by 45k • written 2.4 years ago by ▴ 380
3
votes
5
replies
1.5k
views
Using t test to compare z-scores from RNA expression data
expression Statistics Z-Score RNA
2.4 years ago by Camilo Andres ▴ 40
2
votes
3
replies
1.1k
views
Using RNA-seq to detect pathogen sequences in host tissue
RNA-seq
2.4 years ago by erik.burchard ▴ 30
0
votes
0
replies
689
views
News: Virtual Genome Annotation Workshop
annotation genome workshop
2.4 years ago by mia.nahom ▴ 10
0
votes
0
replies
878
views
Job: Ensembl Production Project Leader
ensembl
updated 2.3 years ago by 45k • written 2.4 years ago by ▴ 30
7
votes
1
reply
1.1k
views
How to plot combined bar graph in R
barplot R singleR ggplot
updated 2.4 years ago by 45k • written 2.4 years ago by ▴ 30
5
votes
6
replies
1.7k
views
Inquiry Regarding Somatic Analysis and Normal Sample Requirement
ngs somatic germline
updated 2.4 years ago by 45k • written 2.4 years ago by ▴ 70
0
votes
0
replies
546
views
Allowed Deviations in fixed bond length and bond angles in peptides from the typical values.
protein bondangles structure fragbuilder python
2.4 years ago by physicsvigna • 0
3
votes
3
replies
2.5k
views
Off-target % for whole-exome sequencing panel
WES
updated 2.4 years ago by ★ 2.0k • written 2.4 years ago by ▴ 170
2
votes
1
reply
732
views
Transcript Directionality with Unstranded Single End Reads ?
transcriptomics expression gene salmon rna-seq
updated 2.4 years ago by 89k • written 2.4 years ago by • 0
0
votes
3
replies
1.2k
views
Extracting information from VCF file for many specific positions in specific chromosomes
SNP RNA GATK seq
updated 2.4 years ago by 166k • written 2.4 years ago by ▴ 30
0
votes
1
reply
1.3k
views
Correcting for continuous covariates before WGCNA
WGCNA
updated 2.4 years ago by 5.1k • written 2.4 years ago by ▴ 10
2
votes
3
replies
1.6k
views
Removing four columns with the same name and position from 38 data.frames in R
Loop remove R columns data.frame
updated 2.4 years ago by 12k • written 2.4 years ago by ▴ 30
4
votes
6
replies
2.5k
views
'position-aware' aligning of sequences with letter annotations
python biopython alignment pairwise
2.4 years ago by Joe 22k
1
vote
0
replies
1.4k
views
Herald: The Biostar Herald for Tuesday, May 23, 2023
herald
2.4 years ago by Biostar 3.6k
1
vote
2
replies
1.1k
views
Identifying/Annotating Enhancers
bedtools R ENCODE
updated 2.3 years ago by 45k • written 2.4 years ago by ▴ 110
0
votes
1
reply
896
views
How to find marker genes for whole tissue from several different sub-tissue scRNAseq datasets
prediction marker scRNAseq
updated 2.4 years ago by ★ 1.9k • written 2.4 years ago by ▴ 60
7
votes
6
replies
4.3k
views
Downloading bulk coding sequences from NCBI that include the organism name in the sequence header?
efetch edirect ncbi
updated 2.4 years ago by 154k • written 2.4 years ago by ▴ 20
1
vote
2
replies
1.1k
views
WGCNA module-trait correlation heatmap has horizontal streaks -- how to interpret/fix?
WGCNA
updated 2.4 years ago by 5.1k • written 2.4 years ago by • 0
1
vote
1
reply
846
views
merging structural variants from various callers into one vcf file (long read sequencing)
vcf longread
updated 2.4 years ago by 5.1k • written 2.4 years ago by ▴ 20
5
votes
4
replies
1.6k
views
How to Split 3000 WGS CRAM files into 1Mbp length chunks
CRAM
updated 2.4 years ago by ★ 4.3k • written 2.4 years ago by • 0
0
votes
0
replies
520
views
extracting gencode 3utr and 5utr as part of R pipeline
5utr 3utr
2.4 years ago by Jalil Sharif ▴ 80
1
vote
2
replies
1.3k
views
Retrieving information from COSMIC database in an automated way
cancer COSMIC variant-calling SNP
updated 2.4 years ago by ▴ 10 • written 2.4 years ago by ▴ 40
19
votes
15
replies
3.0k
views
6 follow
Forum: Cross out line in Biostars
meta
updated 2.4 years ago by 45k • written 7.4 years ago by 6.5k
0
votes
1
reply
952
views
which options to select with UMI-tools and BCLconvert for deduplication of reads
deduplication
updated 2.4 years ago by 22k • written 2.4 years ago by • 0
2
votes
5
replies
1.9k
views
Pre-processing for Agilent microarray data?
affymetrix microarray gene agilent rna
updated 23 months ago by ★ 1.3k • written 2.4 years ago by • 0
0
votes
2
replies
2.5k
views
Trouble annotating heatmap with pheatmap. Error in annotation_col[colnames(mat), , drop = F] : subscript out of bounds
pheatmap
2.4 years ago by oleksandra.kalnytska • 0
28
votes
11
replies
21k
views
9 follow
Salary For A Bioinformatics Programmer In Europe?
career
updated 2.4 years ago by 45k • written 14.1 years ago by 2.3k
0
votes
0
replies
395
views
statistical comparison between accession based on their origins
ttest ANVOA
updated 2.4 years ago by 154k • written 2.4 years ago by • 0
2
votes
1
reply
1.2k
views
Pivot Table Help: A 'VALUE' Filters object has matched 10 row(s). Should have matched at most one row
R Pivottabler
updated 2.4 years ago by 12k • written 2.4 years ago by ▴ 110
0
votes
1
reply
797
views
Phenotype and organism model references for a large list of genes
database
updated 2.4 years ago by 166k • written 2.4 years ago by ▴ 30
1
vote
2
replies
1.6k
views
RSAT, meme to transfac conversion problem
meme transfac
updated 2.4 years ago by • 0 • written 4.1 years ago by ▴ 880
0
votes
3
replies
2.1k
views
Splitting of VCF file of CSQ field in the INFO column to tabular format.
VCF
updated 12 months ago by ★ 4.4k • written 2.4 years ago by • 0
2
votes
5
replies
2.1k
views
Unable to install Cluster Profiler through Docker File
Docker ClusterProfiler
updated 2.4 years ago by 45k • written 2.4 years ago by ▴ 20
0
votes
1
reply
774
views
BED file showing an error while performing the FPKM count in Galaxy Europe
RNASeqdatanalysis galaxyeu fpkmcount
updated 2.4 years ago by 89k • written 2.4 years ago by • 0
1
vote
4
replies
1.7k
views
compression of FASTQ files
fastq
2.4 years ago by kshah.bch • 0
0
votes
0
replies
677
views
LAD/TAD and recombination hotspot data
hotspot recombination lad tad
2.4 years ago by Alex Reynolds 36k
9
votes
5
replies
10k
views
Decoding MM and ML tags in .SAM file
samtools Methylation SAM
updated 21 months ago by ▴ 20 • written 2.4 years ago by ▴ 20
5
votes
6
replies
5.1k
views
Convert Nanopore Fast5 files to Fasta format
fast5 fasta Nanopore
2.4 years ago by Sowmya Pulapet ▴ 70
7
votes
7
replies
10k
views
6 follow
filtering the reads based on the length
RNA-Seq
updated 2.4 years ago by ▴ 400 • written 7.0 years ago by ▴ 10
0
votes
6
replies
2.9k
views
Problem with GPU guppy_basecaller and SLURM
nanopore guppy
2.3 years ago by kenneditodd ▴ 50
3
votes
2
replies
2.2k
views
interpreting inversions on IGV
inversion long-reads igv
2.4 years ago by Shaghayegh ▴ 20
0
votes
2
replies
1.9k
views
Hardy-Weinberg Equilibrium and MAF filtering post imputation
QC beagle imputation
updated 2.4 years ago by 4.8k • written 3.9 years ago by • 0
121,990 results • Page 255 of 2440
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Answer: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions
Answer: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions
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Answer: Quantification using salmon in alignment-based mode after minimap2 run
Comment: Quantification using salmon in alignment-based mode after minimap2 run
Answer: Corresponding BAM files
Answer: Tools To Calculate Average Coverage For A Bam File?
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Recent Replies
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…
Comment: scVI vs Harmony, which is better for cell type based clustering in brain tissue? by Arup Ghosh 3.4k
Try the references from the following publications. https://www.nature.com/articles/s41591-024-03150-z https://www.science.org/doi/10.112…
Answer: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions by Phil Ewels ★ 1.5k
There's an easier way than manually renaming the output files (though you can do this, and it works) - you can use the `name` (aka `stageAs…
Answer: ::Last Call:: In-Person Workshop - NGS Epigenomics Data Analysis (November 3-5 i by ecSeq Bioinformatics ▴ 20
Last Call for this event. Apply now, if you like to join.
Comment: Difficulty running FoldX in linux by Mensur Dlakic ★ 30k
The program is definitely working. It doesn't matter that it didn't produce `TER` and `END` lines at the end. Those are optional in PDB fil…
Answer: Best set of tools / workflows for predicting the biosynthesis pathways of comple by ehaag ▴ 100
I tried [searching for tools in the NIAID Data Ecosystem][1] and found something that may be relevant. [PathPred][2] is an enzyme catalyzed…
Comment: Tools to simulate Illumina short read sequences and ONT long reads with a refere by ehaag ▴ 100
I did a quick [search for tools in the NIAID Data Ecosystem][1] and found a few that map Illumina short reads onto a reference genome, incl…
Answer: Corresponding BAM files by GenoMax 154k
You can get BAM files for 10x single-cell data and they can be found under the `Data Access` tab of the SRA record under the `Original Form…
Comment: GTF file for HIV strain pNL4-3 by Ales ▴ 50
All of the genome assemblies are from the LANL compendiu, match accession with GENBANK (>2,000 complete genome assemblies from the 2021 LAN…
Comment: Hisat2 splice sites extract blank files by Ales ▴ 50
hisat2_extract...py scripts make several assumptions about the input GTF files. For example, they require gene_id field to be present for a…
Comment: GTF file for HIV strain pNL4-3 by GenoMax 154k
> This project started from my personal need to improve spliced alignment Are there plans to submit these annotations to NCBI/EBI? Are yo…
Comment: Hisat2 splice sites extract blank files by Ales ▴ 50
Interestingly, HIV/SIV specifically does have quite an elaborate splicing system which regulates translation. However, only one of the spli…
Answer: Analyzing CRISPR and RNAi genome wide screens by Meisam ▴ 250
I'm late to the party but in case someone has the same question: one practical approach is using **rank-based** methods to meta-analyse you…
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