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1,000 results • Page 4 of 20
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7
votes
8
replies
3.8k
views
DEseq2 design matrix with 3 factors
RNA-seq deseq2
updated 5 months ago by 41k • written 3.5 years ago by ▴ 60
0
votes
8
replies
1.4k
views
What current tools are used to phase haplotypes from a FASTQ file?
phasing haplotypes genomics
updated 9 months ago by 41k • written 2.2 years ago by • 0
2
votes
8
replies
787
views
VCF file CSQ flag
vcf exome-sequencing
updated 5 months ago by 41k • written 5 months ago by ▴ 140
0
votes
8
replies
2.3k
views
Synthetic Human Single Cell Data For Phylogenetic Analysis
phylogenetics
updated 9 months ago by 41k • written 11.0 years ago by • 0
4
votes
8
replies
2.2k
views
6 follow
building snpEff database
snpEff
updated 9 months ago by 41k • written 19 months ago by ▴ 30
3
votes
8
replies
2.4k
views
ANNOVAR ability to report reference and mutant codon
vcf Variant Annovar
updated 11 months ago by 41k • written 8.5 years ago by ▴ 10
5
votes
8
replies
834
views
conda: command not found: gatk.
conda gatk
5 months ago by bestone ▴ 20
1
vote
8
replies
638
views
How does one access TCGA controlled data in AWS S3?
tcga aws
updated 6 weeks ago by ★ 1.1k • written 7 weeks ago by ▴ 10
4
votes
8
replies
1.8k
views
How to extract promoter sequences from a plant draft genome?
promoter genome
updated 6 months ago by 41k • written 4.2 years ago by ▴ 120
1
vote
8
replies
2.3k
views
Using NCBIs EDirect to download pubmed abstract
edirect pubmed NCBI
updated 5 months ago by 41k • written 5.4 years ago by • 0
4
votes
8
replies
1.1k
views
Modeling RNAseq batch effects using a non-case/control technical replicate
batch-correction batch-effect RNA-seq
updated 9 months ago by ★ 16k • written 9 months ago by 22k
1
vote
8
replies
987
views
Retrieve count table from bam file using genomic coordinates
Sequence Htseq-count feature analysis counts
updated 10 months ago by ★ 1.4k • written 10 months ago by • 0
0
votes
8
replies
4.2k
views
Downloading single cell data from NCBI
ncbi rna-seq fastq-dump single-cell
updated 3 months ago by 41k • written 4.9 years ago by ▴ 380
1
vote
8
replies
1.1k
views
Downloading NT chunks from NCBI and creating a BLAST database
nucleotide blast nt blastn database_update.pl
updated 10 months ago by ▴ 90 • written 10 months ago by • 0
0
votes
8
replies
1.5k
views
Cannot process all the reads in a fast5 file?
metagenome nanopore basecalling fastq
6 weeks ago by Gio • 0
0
votes
8
replies
1.7k
views
Chromosome Location of Sequence in Fasta File using Biopython
biopython python
updated 5 months ago by 41k • written 4.0 years ago by • 0
4
votes
8
replies
2.1k
views
Select only sequences that align with X% of a query during blastp search
sequence blast alignment
updated 10 months ago by 41k • written 8.5 years ago by ★ 2.8k
0
votes
8
replies
1.0k
views
Creating fastq subsets from existing files
scRNA-seq umi_tools cellranger fastq
3 months ago by Zack • 0
1
vote
8
replies
2.1k
views
Loading a pre-filtered loom file into pySCENIC
scRNA-seq pySCENIC loom
updated 8 months ago by 41k • written 15 months ago by • 0
2
votes
8
replies
2.7k
views
How to convert a database from protein to nucleotide
blastn unix blastx blast
updated 6 months ago by 41k • written 6.7 years ago by • 0
4
votes
8
replies
3.3k
views
How to reduce the number of SNPs for the Lositan software
Lositan SNP
updated 5 months ago by 41k • written 9.1 years ago by • 0
2
votes
8
replies
1.2k
views
When I run Trimmomatic, I continue to get an "unknown trimmer" error and cannot figure out how to fix it.
trimmomatic
updated 9 months ago by 41k • written 10 months ago by • 0
5
votes
8
replies
1.9k
views
SV calling using giraffe/vg
vg Giraffe calling structural variant
updated 4 months ago by ▴ 410 • written 10 months ago by • 0
5
votes
8
replies
1.7k
views
looking for tools to detect RNA contamination in DNA
RNA-Seq DNA-Seq contamination QC
updated 6 weeks ago by • 0 • written 3.3 years ago by ▴ 230
2
votes
8
replies
1.2k
views
Depth of Coverage in Mitochondrial Genome with Samtools
samtools depth-of-coverage Mitochondrial-genome
8 months ago by Lida • 0
1
vote
8
replies
1000
views
Merge vcfs and retain only specific regions
SNPs vcf
updated 8 months ago by 41k • written 8 months ago by ▴ 30
0
votes
8
replies
991
views
BAM header edit with a list of amplicons
samtools BAM
updated 5 months ago by 41k • written 22 months ago by • 0
4
votes
8
replies
1.3k
views
Error while running nf-core/rnaseq pipeline
nf-core RNA-seq
6 months ago by eesha28112001 • 0
1
vote
8
replies
3.1k
views
interval file for picard
picard
updated 11 months ago by 41k • written 8.4 years ago by ▴ 230
4
votes
8
replies
1.3k
views
Proteomic Statistics - FDR vs p-value
FDR proteomics t-test p-value
10 months ago by bhumm ▴ 70
1
vote
8
replies
995
views
Same correlation values obtained at different soft threshold powers in WGCNA signed network analysis
sft wgcna langfelder
7 months ago by Aditi • 0
3
votes
8
replies
1.2k
views
Query regarding extraction of GTF file
gtf gff
updated 12 months ago by 11k • written 12 months ago by ▴ 30
5
votes
8
replies
1.3k
views
snpeff install error
snpeff
updated 6 months ago by 41k • written 7 months ago by ▴ 20
1
vote
8
replies
526
views
Mitochondrial genes - TPM calculation bulk RNA-Seq
TPM RNA-Seq mtDNA
14 days ago by nick_b55 ▴ 10
1
vote
8
replies
774
views
Reads in IGV are mostly in intron regions
Patchseq RNA-seq
5 months ago by Kai_Qi ▴ 130
1
vote
8
replies
513
views
DESEQ2 design in DESeqDataSetFromMatrix: cell and treatment
rna-seq deseq2
11 days ago by pingu77 ▴ 20
2
votes
8
replies
9.8k
views
Size of typical genomic data
genomic
updated 8 months ago by 41k • written 5.5 years ago by 10k
3
votes
8
replies
649
views
getting coding exon information from Ensembl API
Ensembl API
updated 8 months ago by 41k • written 8 months ago by ▴ 30
0
votes
8
replies
1.3k
views
VCF samtools
vcf samtools variant-calling
updated 5 months ago by 41k • written 24 months ago by • 0
1
vote
8
replies
1.1k
views
Betacoronavirus.00.nsq error
biostars-handbook corona
updated 5 months ago by 41k • written 22 months ago by • 0
7
votes
8
replies
8.7k
views
Determining read count
trimmomatic rna-seq trinity
updated 3 months ago by 41k • written 7.6 years ago by ▴ 110
7
votes
8
replies
1.8k
views
How can we time a recent gene duplication event using (neutral?) DNA mutations as molecular clock?
molecular-clock gene-duplication phylogeny
updated 10 months ago by 41k • written 8.6 years ago by ▴ 20
0
votes
8
replies
9.5k
views
how to find a read by name in a bam file
next-gen-sequencing
updated 5 months ago by 41k • written 6.4 years ago by • 0
3
votes
8
replies
652
views
Single read sequence from a .fasta file cannot be aligned/BLASTN-d to my reference
BLAST bowtie2 BWA alignment
3 months ago by cheesefish21 ▴ 10
3
votes
8
replies
1.7k
views
Kallisto mapping paired end
Kallisto mapping
updated 6 months ago by 41k • written 21 months ago by ▴ 20
0
votes
8
replies
954
views
subset data problem
R seurat
4 months ago by Andy ▴ 100
3
votes
8
replies
1.3k
views
Rseqc infer_experiment.py: 0 usable reads sampled and unknown data type
rseqc infer_experiment.py RNA-seq
11 months ago by pubsurfted ▴ 40
0
votes
8
replies
732
views
The inchworm process failed. Trinity running error.
inchworm transcriptome trinity
updated 6 months ago by 136k • written 6 months ago by • 0
0
votes
8
replies
5.4k
views
miRNA annotation from miRBase 21
miRBase gene-annotation next-gen
updated 8 months ago by 41k • written 9.2 years ago by ▴ 140
3
votes
8
replies
1.9k
views
What is the minimum system requement for oxford nanopore read assembly
Assembly
updated 6 months ago by 41k • written 5.1 years ago by • 0
1,000 results • Page 4 of 20
Recent Votes
Answer: 1000 genomes project reference panel - GRCh38
Answer: 1000 genomes project reference panel - GRCh38
Comment: IMPUTE2- Map file for custom reference panel
IMPUTE2- Map file for custom reference panel
IMPUTE2- Map file for custom reference panel
Comment: Tools or R / Python packages to perfom ML models
Comment: Wrong in Deeptools : the enrichment of TSS and TES region are similar when using
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Recent Replies
Answer: GO categorization by Istvan Albert 99k
If you have an organism that lacks the GO to gene mapping then you have to find a way to assign these terms to your genes. Basically your …
Comment: doubt about usage of megahit by Istvan Albert 99k
you have not mentioned what kind of resources you have, how much data you have to process and what the expected genome/transcriptome sizes …
Comment: Problematic fastq files...How can we trust them? by ATpoint 78k
Then tell her to bring proper data. In the lab you also don't use buffers with mold growing in it, and in bioinformatics we don't start wit…
Comment: Problematic fastq files...How can we trust them? by blackadder ▴ 30
Its not my data. An external researcher is visiting and she wanted from us to do some bioinformatics... The samples were not sequenced by u…
Comment: Tools or R / Python packages to perfom ML models by sil_bioinfo ▴ 30
Oh, I understand. Thank you so much for your help! The truth is that there is so much information, so many packages, libraries, tutorials,…
Comment: Tools or R / Python packages to perfom ML models by Matthias Zepper 4.2k
Just to clarify: Many ML models are trained and executed using dedicated software libraries for machine learning and artificial intellige…
Answer: Problematic fastq files...How can we trust them? by ATpoint 78k
> I assume that maybe all these are fixable with a script but my question is, can we trust these files? Is it worth spending time and effor…
Comment: Tools or R / Python packages to perfom ML models by sil_bioinfo ▴ 30
My main idea is to be able to classify patients with active TB, LTBI and healthy patients as well as possible. The problem is that within t…
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp by rpolicastro 12k
They could have saved themselves a ton of money by sequencing this on a miseq.
Comment: Annotate Unplaced Scaffold with Chromosome Information by cmdcolin ★ 3.4k
I think there are tools like ragtag https://github.com/malonge/RagTag that could help. you can also align your reads back to your new assem…
Comment: An incomprehensible error with R package gggenes by ATpoint 78k
It's not stupid, just a bit lazy ;-)
Comment: Adding functional annotation and meta-data of MAKER/BRAKER GFF by ben@f • 0
Hi, did you find an effective solution for this problem? beside Agat and
Comment: An incomprehensible error with R package gggenes by alice005201314 • 0
Thank you. I asked a stupid question.
Answer: An incomprehensible error with R package gggenes by ATpoint 78k
First hit on google: https://stackoverflow.com/questions/73935357/error-in-grid-callc-convert-x-as-integerwhatfrom-as-integerwhatto-vie
Answer: Should I scale all genes in single cell Seurat? by antonioggsousa 3.0k
Hi, Scaling all features might be useful to plot genes that are not among the 2k HVG in a heatmap. Otherwise than that, I never encounter…
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