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682 results • Page 1 of 14
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76
votes
72
replies
20k
views
19 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
24 days ago by Kevin Blighe 88k
29
votes
28
replies
34k
views
11 follow
Split Fastq Files Into Chunks Of 1M Reads
split fastq
updated 16 days ago by • 0 • written 12.8 years ago by ★ 1.7k
38
votes
24
replies
2.3k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq STAR NGS Illumina
updated 19 days ago by 19k • written 21 days ago by ▴ 580
9
votes
23
replies
9.8k
views
Tool: BioLabDonkey - new Mac program for molecular biologists
software biolabdonkey
8 days ago by vytarasov ▴ 180
8
votes
16
replies
1.2k
views
How to convert plink files to Hapmap Format
GWAS Plink
updated 22 days ago by ★ 2.5k • written 10 weeks ago by • 0
1
vote
16
replies
736
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast ncbi
updated 22 hours ago by 142k • written 3 days ago by • 0
7
votes
16
replies
959
views
How many reads for WGS Sequencing?
WGS Bacterial-Genomics
20 days ago by Ruqaiya • 0
10
votes
16
replies
17k
views
7 follow
How Can I Count Snps In My Final Vcf Files
SNP
updated 12 days ago by 161k • written 5.8 years ago by ▴ 180
4
votes
15
replies
1.7k
views
how to test for differential expression in samples where a global increase in gene expression is expected
edgeR DESeq Differential-Expression RNA-Seq
updated 15 days ago by ★ 7.2k • written 5 months ago by ▴ 10
1
vote
14
replies
2.5k
views
Extract gRNA sequence using cutadapt
cutadapt trimming crispr sequencing
updated 16 days ago by 142k • written 4.5 years ago by ▴ 20
10
votes
14
replies
800
views
6 follow
Bacterial plasmid analysis
bacteria plasmid wgs hybridassembly sequencing
updated 12 days ago by 142k • written 17 days ago by • 0
13
votes
14
replies
963
views
High Malat-1 expression in single cell data
single-cell
updated 11 days ago by ▴ 40 • written 20 days ago by ▴ 40
2
votes
14
replies
3.0k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 5 days ago by • 0 • written 4.8 years ago by ▴ 60
5
votes
13
replies
2.0k
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R Ubuntu Linux Bioconductor Rstudio
updated 28 days ago by 82k • written 4 weeks ago by ★ 1.7k
9
votes
13
replies
4.8k
views
Custom Reference panel creation for data imputation from .vcf files
imputation reference panel
updated 8 days ago by ▴ 50 • written 6.4 years ago by ▴ 490
0
votes
13
replies
3.6k
views
6 follow
Tax4Fun2 - error
tax4fun silva blast
updated 25 days ago by • 0 • written 2.3 years ago by ▴ 10
38
votes
12
replies
31k
views
9 follow
How to systematically check if a bam file is truncated
Exomeseq
updated 1 day ago by ▴ 170 • written 7.1 years ago by ▴ 240
16
votes
12
replies
7.5k
views
10 follow
how to split multi-fasta file into single fasta file named by header
genome perl python3 bash python
updated 16 days ago by ▴ 10 • written 3.2 years ago by ▴ 120
4
votes
12
replies
4.9k
views
10 follow
How to analyze Infinium Mouse Methylation BeadChip array data?
Methylation Experience Illumina Mouse
updated 9 days ago by ▴ 180 • written 3.0 years ago by ▴ 20
4
votes
11
replies
898
views
Redirection of Duplicate PMIDs
pubmed pmid
updated 25 days ago by 4.2k • written 26 days ago by • 0
1
vote
11
replies
5.6k
views
Truncated Bam Error
R next-gen sequencing software error
updated 13 days ago by • 0 • written 6.2 years ago by ▴ 20
2
votes
11
replies
709
views
DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts in whole blood: is it normal to always get NS?
rstudio DEG limma
2 days ago by egascon • 0
19
votes
11
replies
14k
views
10 follow
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
utr
updated 22 days ago by ★ 3.8k • written 10.8 years ago by ▴ 920
25
votes
11
replies
3.8k
views
6 follow
Forum: Site Use Guidelines
meta biostars Guidelines
updated 25 days ago by 43k • written 14.6 years ago by 100k
0
votes
11
replies
721
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo scRNA-seq STAR snRNA-seq MGI
23 days ago by atowns21 • 0
0
votes
11
replies
553
views
In IGV is this a heterogeneous mutation or false call?
mutations IGV heterogeneous
6 days ago by Tuck898 • 0
2
votes
11
replies
1.0k
views
Questions about a bug when transferring cram file to bam file
sequence samtools bcftools
updated 20 days ago by ★ 1.2k • written 4 weeks ago by • 0
40
votes
10
replies
43k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma sva Combat batch-effect
updated 19 days ago by ▴ 40 • written 6.8 years ago by ★ 1.3k
1
vote
10
replies
901
views
error to run rnammer
phylogenomics rRNA_extraction rnammer
updated 13 days ago by • 0 • written 4 months ago by ▴ 30
0
votes
10
replies
641
views
Low mapping rate with Salmon
RNA-seq Salmon Quantification
updated 19 days ago by 19k • written 26 days ago by • 0
1
vote
10
replies
1.1k
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq DESeq2 DNA-contamination
24 days ago by DKA ▴ 40
4
votes
9
replies
456
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch alignment
1 day ago by Gabriel R. ★ 2.9k
1
vote
9
replies
407
views
UMI-Tools knee-method has great influence on the results of white list
single-cell whitelist UMI RNA UMI-Tools
updated 8 days ago by 19k • written 12 days ago by ★ 1.8k
2
votes
9
replies
944
views
TCGA2STAT Error: Firehose connection
FIREHOSE TCGA
updated 25 days ago by 4.2k • written 7 months ago by • 0
0
votes
9
replies
1.5k
views
kinannote software installation problems
kinannote
updated 10 days ago by • 0 • written 5.8 years ago by ▴ 30
4
votes
9
replies
2.2k
views
6 follow
Same sequencing sample in multiple lanes. How to analyse it?
sequencing bowtie2 alignment samtools ngs
updated 15 days ago by • 0 • written 2.2 years ago by • 0
0
votes
9
replies
2.6k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome base-calling fastq nanopore
updated 20 days ago by 43k • written 9 months ago by • 0
0
votes
9
replies
360
views
Duplicated reads (IDs) from nanopore sequencing
bam nanopore sequencing
3 days ago by njornet ▴ 20
2
votes
9
replies
716
views
Filtering Multi-sample VCF file for all except one Genotype
variant SNP VCF
updated 4 days ago by 161k • written 11 days ago by • 0
4
votes
9
replies
2.7k
views
Tool: CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
RNA-Seq
written 8.3 years ago by • 0
3
votes
9
replies
629
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 25 days ago by 100k • written 26 days ago by • 0
0
votes
9
replies
606
views
Using VEP annotation output as the input for a second VEP annotation
Annotation VEP VCF
3 days ago by Arton ▴ 10
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference 38build impute imputation
19 days ago by anna ▴ 20
0
votes
9
replies
627
views
Applying the metacell2 algorithm using python
python single-cell scanpy metacell2
updated 3 days ago by ★ 2.0k • written 12 days ago by ▴ 140
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk genomicsdbimport
updated 16 days ago by • 0 • written 5.1 years ago by 11k
2
votes
8
replies
388
views
joint callset and vcf sorting, unknown TAG issue
sort bcftools GLNexus merge VCF
updated 6 days ago by 161k • written 7 days ago by ▴ 100
3
votes
8
replies
1.4k
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq Cellranger STARsolo 10X
updated 29 days ago by 14k • written 9 months ago by ▴ 80
4
votes
8
replies
774
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs BED eqtl bedtools
updated 22 days ago by 35k • written 23 days ago by ▴ 10
3
votes
8
replies
713
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core 16S amplicon dada2 ampliseq
updated 12 days ago by ▴ 410 • written 16 days ago by ▴ 100
0
votes
8
replies
542
views
What does it mean single base resolution in sequencing?
SNP sequencing
updated 18 days ago by 4.2k • written 20 days ago by ▴ 10
682 results • Page 1 of 14
Recent Votes
plotting trees in R: node labels from nexus tree files
Interpreting the Jackstraw plot of Seurat
A: How is the design in DESeq2 work?
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
Answer: RNAseq coverage vs depth for transcript isoform expression?
constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
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Comment: Add stats to the plot by marco.barr ▴ 130
Hi, you can add statistical annotations using `ggpubr` function `stat_pvalue_manual `. You need to make sure you calculate the p-values fir…
Answer: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from by ATpoint 82k
Use everything before the whitespace in list.txt, for example `A00869:294:HCW57DSXY:2:1101:3929:1000` and not `A00869:294:HCW57DSXY:2:1101:…
Answer: CellRanger output more cells than specified using --force-cells? Why? by scideas ▴ 30
I actually had this same issue with CellRanger v7- turns out that since you have 2 species in your mapping reference, CellRanger is forcing…
Answer: Checking chromosome builds for genotyping data by Muhammad • 0
Assume you have genotype data in Plink format. (G.bed, G.bim, G.fam) Download some reference panel data in Plink format (R.bed, R.bim, R.f…
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors) by nguyenn6 • 0
did you ever figure it out? i'm having the same issue.
Comment: Traveler with Infernal mapping failed by anton.i.petrov • 0
Hi Larissa! I am the lead developer of R2DT and I've just noticed this question. Could you please email help@r2dt.bio with your input seque…
Comment: constructing pangenome through psvcp by analyst ▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by GenoMax 142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
Comment: calculating genomic coverage/ base overlap in R by 1769mkc ★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks by ATpoint 82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner by Joe 21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression? by Gordon Smyth ★ 7.2k
See the exploration of isoform estimation precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167.…
Comment: How to handle duplicated genes in TCGA data? by txema.heredia ▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA by mavy ▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by hophuquy0944 • 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
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