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1,000 results • Page 4 of 20
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1
vote
8
replies
2.5k
views
subset data problem
R seurat
9 months ago by Andy ▴ 120
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
5
votes
8
replies
1.9k
views
snpeff install error
snpeff
updated 11 months ago by 43k • written 12 months ago by ▴ 30
3
votes
8
replies
984
views
Single read sequence from a .fasta file cannot be aligned/BLASTN-d to my reference
BLAST bowtie2 BWA alignment
8 months ago by cheesefish21 ▴ 10
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
2.5k
views
Using NCBIs EDirect to download pubmed abstract
edirect pubmed NCBI
updated 10 months ago by 43k • written 5.8 years ago by • 0
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
1.3k
views
Betacoronavirus.00.nsq error
biostars-handbook corona
updated 10 months ago by 43k • written 2.3 years ago by • 0
0
votes
8
replies
1.1k
views
BAM header edit with a list of amplicons
samtools BAM
updated 10 months ago by 43k • written 2.3 years ago by • 0
0
votes
8
replies
4.4k
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
0
votes
8
replies
559
views
STAR aligner options
STAR
4 weeks ago by theophile • 0
5
votes
8
replies
2.4k
views
SV calling using giraffe/vg
vg Giraffe calling structural variant
updated 9 months ago by ▴ 460 • written 15 months ago by • 0
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
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
3
votes
8
replies
622
views
Huge decrease of BUS records using bustools
single-cell bustools 10X
8 weeks ago by julien.wollbrett • 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 12 weeks ago by ★ 16k • written 3 months ago by • 0
2
votes
8
replies
2.9k
views
How to convert a database from protein to nucleotide
blastn unix blastx blast
updated 11 months ago by 43k • written 7.1 years ago by • 0
0
votes
8
replies
1.9k
views
Chromosome Location of Sequence in Fasta File using Biopython
biopython python
updated 10 months ago by 43k • written 4.4 years ago by • 0
5
votes
8
replies
3.7k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression RNA-seq gene-ontology
updated 19 days ago by 43k • written 6.5 years ago by ★ 1.6k
2
votes
8
replies
1.0k
views
VCF file CSQ flag
vcf exome-sequencing
updated 10 months ago by 43k • written 10 months ago by ▴ 160
3
votes
8
replies
909
views
Can these RNAseq runs be combined?
transcriptomics replicates RNAseq
updated 10 months ago by 141k • written 10 months ago by • 0
3
votes
8
replies
2.0k
views
Kallisto mapping paired end
Kallisto mapping
updated 11 months ago by 43k • written 2.2 years ago by ▴ 20
5
votes
8
replies
1.9k
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
0
votes
8
replies
1.5k
views
Cannot find Output files after applying Markduplicates with picard tools
picard-tools MarkDuplicates
updated 6 weeks ago by • 0 • written 19 months ago by • 0
5
votes
8
replies
603
views
Multiple threads on ubuntu server
Ubuntu
updated 3 months ago by 6.4k • written 3 months ago by ▴ 50
0
votes
7
replies
408
views
DESeq: too low p-value for RNAseq
R DESeq p-value RNA-seq FDR
updated 23 days ago by ★ 2.9k • written 24 days ago by ▴ 10
0
votes
7
replies
922
views
Mugsy error -directory must be a directory
Mugsy
updated 7 months ago by 43k • written 3.4 years ago by ▴ 160
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
1
vote
7
replies
3.1k
views
RGT TypeError: unsupported operand type(s) for +: 'NoneType' and 'int'
RGT TF-footprinting ATAC-seq
updated 10 months ago by 43k • written 5.4 years ago by ★ 2.6k
0
votes
7
replies
1.0k
views
All question mark quality scores on several studies
quality-score shotgun illumina
updated 10 months ago by 43k • written 10 months ago by ▴ 10
2
votes
7
replies
554
views
Need a link to OLDERADO server
pdb protein nmr structure
6 weeks ago by b2003 • 0
2
votes
7
replies
4.7k
views
SRA toolkit internet settings
sratoolkit fastq-dump sequencing RNA-Seq
updated 10 months ago by 43k • written 7.7 years ago by ▴ 90
7
votes
7
replies
588
views
6 follow
PCA plot interpretation (single population)
PCA GWAS pruning
12 weeks ago by Shane ▴ 20
0
votes
7
replies
444
views
Salmon Quantification in Alignment based-mode
Salmon RNA-seq TPM
updated 4 weeks ago by 141k • written 4 weeks ago by • 0
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 141k • written 8 months ago by • 0
1
vote
7
replies
894
views
GATK Mutect2 Input files reference and features have incompatible contigs: No overlapping contigs found.
hg19 Mutect2 GATK Variant-Calling
updated 4 weeks ago by 43k • written 9 months ago by ▴ 100
2
votes
7
replies
505
views
How to predication/annotation trans-splicing in genome
trans-splicing genome annotation mitochondrial
12 weeks ago by oasiswho • 0
2
votes
7
replies
663
views
Does removal of contaminants in RNAseq data have an impact on downstream analyses?
RNA-seq contamination
updated 6 weeks ago by ▴ 390 • written 6 weeks ago by ▴ 20
4
votes
7
replies
768
views
Alternative for grep in a for loop
linux
updated 6 months ago by 43k • written 6 months ago by ▴ 20
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
456
views
1000 Genome: Cause of duplicate variants with different genotypes
CrossMap 1000Genome 1000G
updated 11 weeks ago by ▴ 390 • written 11 weeks ago by ▴ 210
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
11 months ago by sohail.mbio • 0
2
votes
7
replies
851
views
Should we assume UMI-based scRNAseq data is not compositional?
compositional scRNAseq
9 months ago by cwwong13 ▴ 40
0
votes
7
replies
2.2k
views
Command not found after pip install spliceai
software error
updated 6 months ago by • 0 • written 3.5 years ago by • 0
0
votes
7
replies
950
views
Issue with Merging BCF Files: Invalid INFO id Error
bcftools
updated 5 months ago by 43k • written 5 months ago by ▴ 10
1
vote
7
replies
1.9k
views
for loop in a bash script
bash
updated 10 months ago by 43k • written 2.6 years ago by • 0
4
votes
7
replies
2.4k
views
Batch effects vs biological variables
Batch-effect DESeq2 combat_seq
updated 20 days ago by 43k • written 3.7 years ago by ▴ 20
0
votes
7
replies
916
views
SNPeff problem
snpEff
updated 9 months ago by 43k • written 9 months ago by • 0
1
vote
7
replies
527
views
limma eBayes error in analysis of Illumina HumanHT-12 V4.0 expression beadchip data
R beadchip limma microarray Illumina
updated 8 weeks ago by ★ 1.2k • written 8 weeks ago by ▴ 20
10
votes
7
replies
3.7k
views
What is Pathway Analysis?
database analysis ontology pathway
updated 10 months ago by 43k • written 8.0 years ago by ▴ 330
1,000 results • Page 4 of 20
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Comment: How to assign cell types after integration in scRNA
NGS forensics: how to know if data is fabricated
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Recent Replies
Comment: What does it mean single base resolution in sequencing? by dsull ★ 5.9k
Great comprehensive explanation and overview of the technologies -- with regards to sequencing assays, the one thing I'd add is SNV identif…
Answer: What does it mean single base resolution in sequencing? by dsull ★ 5.9k
I think that term means slightly different things in different contexts. For example, it's useful to profile mRNA modifications (e.g. m6a) …
Answer: Cannot process all the reads in a fast5 file? by chujie • 0
Hi, I met the same problem, have you found the solution?
Answer: What does it mean single base resolution in sequencing? by LauferVA 4.2k
Hi @fe3e6f65 , In a single sentence, the answer to your question can be summarized as, "*the resolution of a genomic technology refers to …
Comment: PCA plot by LauferVA 4.2k
Without more context, we cannot interpret this PCA plot. There are many possibilities. In addition, this question is basic enough that it w…
Comment: NGS forensics: how to know if data is fabricated by Jeremy Leipzig 22k
i have the name ready: out**liar**
Comment: What does it mean single base resolution in sequencing? by GenoMax 141k
Sequencing by hybridization (https://en.wikipedia.org/wiki/Sequencing_by_hybridization ) is likely not giving you single base resolution. B…
Comment: Fetch table from clinvar database according to a list of rsid by ashaneev07 ▴ 20
Hii... i have updated the script in python..But, still getting no data found. Actually the data is there, i have print the parsed html file…
Comment: How to assign cell types after integration in scRNA by ATpoint 82k
https://bioconductor.org/books/release/OSCA.multisample/using-corrected-values.html
Comment: Downloading full alignments from Pfam by GenoMax 141k
Not as convenient but the entire set of full alignments can be downloaded here: https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pf…
Comment: How many reads for WGS Sequencing? by GenoMax 141k
> What does clipped Fastq mean? Probably means that NCBI has already scanned and trimmed adapter sequencers. > both forward and revers…
Comment: How many reads for WGS Sequencing? by GenoMax 141k
You can use the default `adapters.fa` file included in the `resources` folder of [**BBMap suite**][1] (program to use is `bbduk.sh`) or a p…
Comment: How many reads for WGS Sequencing? by GenoMax 141k
Only way to find out is to try. It may work but if it is not going to then you will find that out quick (process would likely crash because…
Comment: How many reads for WGS Sequencing? by Ruqaiya • 0
Also, there is no mention of adapter sequence so which adapter sequence should i use to remove it from some other reads?
Comment: How many reads for WGS Sequencing? by Ruqaiya • 0
Also, Do you think i can reproduce at least most part of the data from the paper just on my laptop? It has 4 logical processors (Intel(R) C…
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