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1,000 results • Page 4 of 20
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4
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8
replies
1.9k
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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
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
625
views
GCP Snakemake
snakemake GCP
updated 3 months ago by 43k • written 3 months ago by ▴ 10
1
vote
8
replies
1.5k
views
counts of cite-seq-count vs. cellrenager varies tremendously
citeseq-count cellranger cite-seq scRNA-seq
updated 4 months ago by 82k • written 9 months ago by ★ 1.8k
1
vote
8
replies
1.1k
views
How does one access TCGA controlled data in AWS S3?
tcga aws
updated 7 months ago by ★ 1.2k • written 7 months ago by ▴ 10
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
6
votes
8
replies
1.2k
views
conda: command not found: gatk.
conda gatk
11 months ago by bestone ▴ 30
5
votes
8
replies
641
views
Multiple threads on ubuntu server
Ubuntu
updated 3 months ago by 6.4k • written 3 months ago by ▴ 50
5
votes
8
replies
1.0k
views
sc-RNA seq pipeline
scRNA-seq NGS RNA-Seq
4 months ago by Researcher ▴ 30
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 26 days ago by 43k • written 7.0 years ago by ▴ 20
2
votes
8
replies
1.1k
views
VCF file CSQ flag
vcf exome-sequencing
updated 11 months ago by 43k • written 11 months ago by ▴ 160
0
votes
8
replies
674
views
Phobius error: Could not read provided fasta sequence at phobius.pl line 408
Phobius
updated 10 weeks ago by ▴ 10 • written 3 months ago by ▴ 30
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
0
votes
8
replies
1.9k
views
Chromosome Location of Sequence in Fasta File using Biopython
biopython python
updated 11 months ago by 43k • written 4.5 years ago by • 0
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
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
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
1
vote
8
replies
3.9k
views
No gene can be mapped
R GSEA
updated 4 months ago by ★ 1.8k • written 2.3 years ago by • 0
1
vote
8
replies
863
views
DESEQ2 design in DESeqDataSetFromMatrix: cell and treatment
rna-seq deseq2
5 months ago by pingu77 ▴ 20
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
519
views
Downsampling fastq file
downsample fastq
13 days ago by marco.barr ▴ 100
5
votes
8
replies
2.0k
views
looking for tools to detect RNA contamination in DNA
RNA-Seq DNA-Seq contamination QC
updated 6 months ago by • 0 • written 3.7 years ago by ▴ 230
1
vote
8
replies
1.1k
views
Mitochondrial genes - TPM calculation bulk RNA-Seq
TPM RNA-Seq mtDNA
5 months ago by nick_b55 ▴ 10
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
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk genomicsdbimport
updated 11 days ago by • 0 • written 5.1 years ago by 11k
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
935
views
Can these RNAseq runs be combined?
transcriptomics replicates RNAseq
updated 10 months ago by 142k • written 10 months ago by • 0
1
vote
7
replies
565
views
limma eBayes error in analysis of Illumina HumanHT-12 V4.0 expression beadchip data
R beadchip limma microarray Illumina
updated 10 weeks ago by ★ 1.2k • written 10 weeks ago by ▴ 20
0
votes
7
replies
659
views
Using Primer3 with python to genotype a SNP at a particular position
primer3 python position primer
updated 5 months ago by 161k • written 5 months ago by • 0
0
votes
7
replies
986
views
Issue with Merging BCF Files: Invalid INFO id Error
bcftools
updated 5 months ago by 43k • written 5 months ago by ▴ 10
0
votes
7
replies
956
views
For loop RNA Sequencing alignment
RNA STAR
updated 10 months ago by 43k • written 19 months ago by • 0
0
votes
7
replies
932
views
Mugsy error -directory must be a directory
Mugsy
updated 7 months ago by 43k • written 3.4 years ago by ▴ 160
1
vote
7
replies
3.1k
views
RGT TypeError: unsupported operand type(s) for +: 'NoneType' and 'int'
RGT TF-footprinting ATAC-seq
updated 11 months ago by 43k • written 5.4 years ago by ★ 2.6k
0
votes
7
replies
937
views
SNPeff problem
snpEff
updated 10 months ago by 43k • written 10 months ago by • 0
3
votes
7
replies
512
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
616
views
Trying to extract .cram file read sequences into array
CRAM pysam reads samtools
11 weeks ago by sacryt • 0
2
votes
7
replies
1.4k
views
VG mapping paired-end reads: error [xg]: multiple hits for XXX
variation-graph reads pangenome vg paired-end
8 months ago by nkls063408 • 0
2
votes
7
replies
935
views
Removing duplicates
duplicates ONT minimap2
updated 24 days ago by ▴ 580 • written 26 days ago by • 0
2
votes
7
replies
701
views
Does removal of contaminants in RNAseq data have an impact on downstream analyses?
RNA-seq contamination
updated 8 weeks ago by ▴ 410 • written 8 weeks ago by ▴ 20
0
votes
7
replies
532
views
Using VEP annotation output as the input for a second VEP annotation
VCF VEP Annotation
updated 8 weeks ago by 43k • written 3 months ago by • 0
1
vote
7
replies
1.5k
views
Typical percentage of multimapping reads in human rna-seq?
RNA-seq alignment Bowtie2 STAR
updated 10 months ago by 142k • written 10 months ago by ▴ 60
0
votes
7
replies
1.4k
views
fasterq-dump outputs "Cannot use '--ngc' as ngc file."
snakemake sra-tools SRA
updated 10 months ago by 43k • written 12 months ago by ▴ 80
4
votes
7
replies
2.7k
views
low bootstrap value?
phylogeny genome alignment
updated 11 months ago by 43k • written 4.9 years ago by ▴ 120
0
votes
7
replies
2.0k
views
CIBERSORTx error: 'x' must be an array of at least two dimensions
matrix CIBERSORTx signature
updated 5 months ago by • 0 • written 22 months ago by • 0
4
votes
7
replies
631
views
Can any JBrowse2 tracks show multiple colors for reads at different nucleotide positions?
JBrowse JBrowse2
updated 5 weeks ago by ★ 3.8k • written 6 weeks ago by ▴ 140
10
votes
7
replies
3.7k
views
What is Pathway Analysis?
database analysis ontology pathway
updated 11 months ago by 43k • written 8.1 years ago by ▴ 330
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
578
views
Iterate through Seurat object to add patient information
R Seurat
updated 3 months ago by 43k • written 3 months ago by ▴ 100
3
votes
7
replies
529
views
How does kallisto handle multi mapped reads?
kallisto
updated 11 weeks ago by ★ 6.0k • written 11 weeks ago by ▴ 150
1,000 results • Page 4 of 20
Recent Votes
Best way to query VCF for specific variants
Comment: featureCounts output summary assigned value higher than uniquely mapped reads fr
A: Is Bam One-Based Or Zero-Based?
A: Is Bam One-Based Or Zero-Based?
A: Data Set Suitable For Comparing Wgs, Exome, And Rna-Seq Data Generated From The
Answer: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read
Practical Haplotype Graph v2 not finding correct paths
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Recent Replies
Comment: Extracting named fasta sequences according to list with Biopython by Rubayetul • 0
the last line of SeqIO.write(record.....'fasta') in a for loop will input the the last record into new fasta file and it will only contain …
Comment: How to process Bulk WES data? by GenoMax 142k
You could use `sarek` (nf-core's exome pipeline) if you don't want to customize or reinvent : https://nf-co.re/sarek/3.4.2
Comment: Empty .best and .sing2 Files After Running Demuxlet by Ram 43k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Answer: FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last plac by David Langenberger 11k
Two last seats have just become available. Apply now, if you want them.
Comment: featureCounts output summary assigned value higher than uniquely mapped reads fr by GenoMax 142k
You always need to add the following option when you are using `-p` to count paired-end reads. --countReadPairs If specified, fragm…
Comment: Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so t by mropri ▴ 150
Hi swbarnes2, that was the problem, they were not numeric but as character columns. converted them and it fixed the error. Thank you for yo…
Answer: featureCounts output summary assigned value higher than uniquely mapped reads fr by Prawesh • 0
I figured out: Since featureCounts counts fragments and not reads, we have pair-end data that means **Assigned** value from the output w…
Answer: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read by kalavattam ▴ 190
> My question is this: "mate reverse strand" (flag 16/0x10) or "read reverse strand" (flag 32/0x20) do not directly relate to the strandedn…
Answer: How to interpret infinite odds ratio? by bhumm ▴ 140
As you stated, your problem is likely division by 0. See this [Cross-Validated][1] post that seems to be very similar to your problem. In …
Comment: Duplicated sequence samtools by GenoMax 142k
Consider using SLURM job arrays if you want to use a `for` loop inside a single SLURM job: https://hpc.nmsu.edu/discovery/slurm/job-arrays/
Answer: Duplicated sequence samtools by Pierre Lindenbaum 161k
the sequence c_000007023807_aloha2_low_cov is duplicated in the reference grep c_000007023807_aloha2_low_cov path/to/reference.fasta
Comment: imputation through beagle by analyst ▴ 50
Thank you so much dthorbur. Yes I am new to imputation analysis. I will follow your kind suggestions. Thanks again!
Answer: Benchmarking RNASeq Variant Calling Pipeline (Short Reads) by lagartija ▴ 160
I don't know but another way of doing it would be to combine different datasets of different strains that you know are clonal. Then you kno…
Comment: consensus sequence calling by bk11 ★ 2.4k
Please check out these posts https://www.biostars.org/p/367626/
Comment: Galaxy StringTie error by trkfs • 0
will do, thank you
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