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1,000 results • Page 4 of 20
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Phobius error: Could not read provided fasta sequence at phobius.pl line 408
Phobius
updated 11 weeks ago by ▴ 10 • written 3 months ago by ▴ 30
1
vote
8
replies
3.9k
views
No gene can be mapped
R GSEA
updated 4 months ago by ★ 1.8k • written 2.4 years ago by • 0
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 3 months ago by ★ 16k • written 3 months ago by • 0
0
votes
8
replies
1.5k
views
VCF samtools
vcf samtools variant-calling
updated 11 months ago by 43k • written 2.4 years ago by • 0
0
votes
8
replies
1.3k
views
Creating fastq subsets from existing files
scRNA-seq umi_tools cellranger fastq
9 months ago by Zack • 0
3
votes
8
replies
2.0k
views
What is the minimum system requement for oxford nanopore read assembly
Assembly
updated 11 months ago by 43k • written 5.5 years ago by • 0
1
vote
8
replies
3.5k
views
Best way to address different batches of RNA-seq
sequence RNA-Seq RPKM Fold-Change batch-effect
updated 27 days ago by 43k • written 7.1 years ago by ▴ 20
3
votes
8
replies
566
views
How to access TCGA samples that were treated with a specific drug?
TCGA RNA-seq
8 days ago by Qroid ▴ 40
5
votes
8
replies
2.5k
views
SV calling using giraffe/vg
vg Giraffe calling structural variant
updated 9 months ago by ▴ 460 • written 16 months ago by • 0
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk genomicsdbimport
updated 12 days ago by • 0 • written 5.1 years ago by 11k
1
vote
8
replies
866
views
DESEQ2 design in DESeqDataSetFromMatrix: cell and treatment
rna-seq deseq2
5 months ago by pingu77 ▴ 20
3
votes
8
replies
937
views
Can these RNAseq runs be combined?
transcriptomics replicates RNAseq
updated 10 months ago by 142k • written 10 months ago by • 0
5
votes
8
replies
1.0k
views
sc-RNA seq pipeline
scRNA-seq NGS RNA-Seq
4 months ago by Researcher ▴ 30
2
votes
8
replies
1.0k
views
HGVS Nomenclature of Multiple Indels found in Cis
Nomenclature HGVS
updated 11 weeks ago by ▴ 560 • written 5 months ago by 4.2k
4
votes
8
replies
1.2k
views
Error executing nf-core/metaboigniter pipeline
nf-core metaboigniter nextflow
updated 8 months ago by ★ 1.4k • written 8 months ago by • 0
0
votes
8
replies
4.5k
views
Downloading single cell data from NCBI
ncbi rna-seq fastq-dump single-cell
updated 8 months ago by 43k • written 5.4 years ago by ▴ 380
5
votes
8
replies
2.0k
views
looking for tools to detect RNA contamination in DNA
RNA-Seq DNA-Seq contamination QC
updated 7 months ago by • 0 • written 3.7 years ago by ▴ 230
0
votes
8
replies
10.0k
views
how to find a read by name in a bam file
next-gen-sequencing
updated 10 months ago by 43k • written 6.8 years ago by • 0
0
votes
8
replies
1.6k
views
Cannot find Output files after applying Markduplicates with picard tools
picard-tools MarkDuplicates
updated 8 weeks ago by • 0 • written 20 months ago by • 0
0
votes
8
replies
593
views
STAR aligner options
STAR
6 weeks ago by theophile • 0
1
vote
8
replies
1.3k
views
Betacoronavirus.00.nsq error
biostars-handbook corona
updated 11 months ago by 43k • written 2.3 years ago by • 0
0
votes
8
replies
1.0k
views
The inchworm process failed. Trinity running error.
inchworm transcriptome trinity
updated 11 months ago by 142k • written 11 months ago by • 0
1
vote
8
replies
2.5k
views
Using NCBIs EDirect to download pubmed abstract
edirect pubmed NCBI
updated 10 months ago by 43k • written 5.9 years ago by • 0
1
vote
8
replies
1.0k
views
Reads in IGV are mostly in intron regions
Patchseq RNA-seq
10 months ago by Kai_Qi ▴ 130
7
votes
8
replies
9.0k
views
Determining read count
trimmomatic rna-seq trinity
updated 8 months ago by 43k • written 8.0 years ago by ▴ 110
3
votes
8
replies
1.0k
views
Single read sequence from a .fasta file cannot be aligned/BLASTN-d to my reference
BLAST bowtie2 BWA alignment
9 months ago by cheesefish21 ▴ 10
2
votes
8
replies
722
views
TCGA Biospecimens Slides Extraction
tcga
updated 11 weeks ago by ★ 1.2k • written 12 weeks ago by ▴ 10
5
votes
8
replies
3.7k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression RNA-seq gene-ontology
updated 5 weeks ago by 43k • written 6.5 years ago by ★ 1.6k
3
votes
7
replies
513
views
Snakemake rule that runs an assessment for once after completing other previous rules
snakemake
9 weeks ago by Fadlilah ▴ 10
0
votes
7
replies
617
views
Trying to extract .cram file read sequences into array
CRAM pysam reads samtools
11 weeks ago by sacryt • 0
0
votes
7
replies
935
views
Mugsy error -directory must be a directory
Mugsy
updated 7 months ago by 43k • written 3.5 years ago by ▴ 160
7
votes
7
replies
1.9k
views
Sort and convert the SAM files to BAM
samtools RNA-seq NGS
updated 8 months ago by 43k • written 5.8 years ago by ▴ 40
4
votes
7
replies
1.1k
views
Statistical test to compare data across timepoints
Statistics
updated 7 months ago by 4.6k • written 7 months ago by ▴ 20
0
votes
7
replies
1.3k
views
FACS (Fluorescence-activated cell sorting NOT cyTOF),Automating the removal of dead and duplicated cells
FACS
updated 7 months ago by ▴ 900 • written 8 months ago by ▴ 20
1
vote
7
replies
1.3k
views
For loop STAR not working
RNA-Seq STAR
updated 10 months ago by 43k • written 2.9 years ago by ▴ 30
1
vote
7
replies
1.6k
views
Accuracy of Methods for Gene Variant Detection and Quantification: Kallisto Pseudoalignment vs. STAR Alignment
kallisto STAR RNA-seq Transcript_variants
12 months ago by sohail.mbio • 0
0
votes
7
replies
1.1k
views
Tool-Compare Sequences within a Single Tree.
mutations sequence alignment
updated 10 months ago by 43k • written 5.2 years ago by • 0
0
votes
7
replies
465
views
Salmon Quantification in Alignment based-mode
Salmon RNA-seq TPM
updated 6 weeks ago by 142k • written 6 weeks ago by • 0
1
vote
7
replies
925
views
GATK Mutect2 Input files reference and features have incompatible contigs: No overlapping contigs found.
hg19 Mutect2 GATK Variant-Calling
updated 7 weeks ago by 43k • written 9 months ago by ▴ 100
0
votes
7
replies
580
views
Iterate through Seurat object to add patient information
R Seurat
updated 3 months ago by 43k • written 3 months ago by ▴ 100
0
votes
7
replies
2.7k
views
How to perform gene annotation in kallisto?
Gene kallisto annotation
updated 8 months ago by • 0 • written 2.7 years ago by ▴ 100
3
votes
7
replies
6.3k
views
running trimmomatic inside Trinity
Assembly Trinity RNA-seq trimmomatic
updated 10 months ago by 43k • written 8.1 years ago by ▴ 50
0
votes
7
replies
7.3k
views
Problem in in alignment by muscle
sequence muscle alignment
updated 10 months ago by 43k • written 6.8 years ago by ▴ 70
2
votes
7
replies
1.8k
views
Technology Stack of NCBI (Genbank, GEO, etc.)
sequence ncbi gene genbank
updated 11 months ago by 43k • written 6.2 years ago by ▴ 70
6
votes
7
replies
1.8k
views
Reference genome for RNA-Seq reads decontamination
FastQ_Screen RNA-Seq
updated 8 months ago by 43k • written 4.2 years ago by ▴ 70
2
votes
7
replies
1.1k
views
error: BLAST database name is missing. Please edit provean.sh file to add the name.
provean error
updated 8 months ago by 142k • written 8 months ago by • 0
4
votes
7
replies
635
views
Can any JBrowse2 tracks show multiple colors for reads at different nucleotide positions?
JBrowse JBrowse2
updated 6 weeks ago by ★ 3.8k • written 6 weeks ago by ▴ 140
0
votes
7
replies
1.2k
views
How to deal with duplicated gene IDs in TCGA RNA expression data?
TCGA Expression mRNA
updated 11 months ago by 4.2k • written 11 months ago by ▴ 40
3
votes
7
replies
1.1k
views
Use giraffe in vg
giraffe vg
updated 10 months ago by ▴ 460 • written 10 months ago by • 0
0
votes
7
replies
781
views
Search for specific SNPs in VCF files of patients.
ANNOVAR vcftools bcftools GATK VCF
updated 4 months ago by 43k • written 4 months ago by ▴ 10
1,000 results • Page 4 of 20
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Comment: Bamutils/ClipOverlap
Comment: How to calculate coverage of Nanopore long read data?
Comment: Overlapping Ranges within Granges object
Answer: Difference between Genotype 0|1 and 1|0 in VCF file?
Answer: how to keep reads in a fasta file based on a seq id list in R?
Answer: The total expressed genes in RNA-Seq data
C: Re-arrange conditions in Seurat
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Recent Replies
Comment: BWA alignment by a.alnawfal.1992 ▴ 260
that's great, but i believe the issue is related to stdin rather than index
Comment: BWA alignment by a.alnawfal.1992 ▴ 260
it is not!!
Comment: How to calculate coverage of Nanopore long read data? by Arton • 0
Thank you! I eventually used the information generated by three tools (samtools coverage+ mosdepth + NanoPlot).
Comment: Alphaphold 3 pLDDT coloring scheme in chimerax? by mbrav005 • 0
Thank you Sir! you are right my model is not very good. Do You know how I can improve the scores. Also I am able to color the structure by …
Comment: Polish a large genome with Pilon by sansan_96 ▴ 90
..........
Comment: Overlapping Ranges within Granges object by ntsopoul ▴ 60
you are on to something… if I use reduce to find the “overlaping regions” in a secon GRanges object, what do I do next?
Comment: Using ggplotly in R by jen ▴ 10
Thank you Jared for your response. I took a look at the documentation you provided and am trying my best to follow along, but can't seem to…
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred by Juke34 8.6k
Right I heard there is an issue since Perl v5.36. You may have better luck using conda. Or the best way is to use the container. Or downgra…
Answer: Alphaphold 3 pLDDT coloring scheme in chimerax? by Mensur Dlakic ★ 27k
pLDDT scores are stored in the so-called B-factor column in PDB files. Below the `File` ribbon select `Molecule Display` and click on `b-fa…
Comment: Genome Visualization Tools by dlera.lozano ▴ 10
Thank you so much
Answer: Doubt about the process of annotation, detection, identification and classificat by Mensur Dlakic ★ 27k
Depends on the context. `TE detection` and `TE identification` could mean the same thing if they refer to presence/absence of TEs. `TE iden…
Comment: featureCounts output summary assigned value higher than uniquely mapped reads fr by Ram 43k
Please accept your own answer to mark the post as solved.
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file by Ram 43k
A small educational note: if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accep…
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file by Prawesh • 0
thanks, it's working now.
Answer: Genome Visualization Tools by GenoMax 142k
@cmdcolin has a great list here: https://github.com/cmdcolin/awesome-genome-visualization
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