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116,634 results • Page 4 of 2333
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3
votes
5
replies
275
views
Per base sequence content error in RNAseq analysis
RNA-seq analysis
updated 5 days ago by 141k • written 6 days ago by • 0
0
votes
0
replies
92
views
Trimming best practices for SNP calling
trimming SNP trimmomatic
5 days ago by Enrique • 0
3
votes
5
replies
554
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align RNA-Seq linux STAR
5 days ago by n_navy • 0
0
votes
0
replies
75
views
Correct way of reducing predictive model complexity
lasso glmnet predictvemodeling regression
5 days ago by sativus ▴ 20
6
votes
3
replies
185
views
Interpretting IGV output
IGV
updated 5 days ago by 8.7k • written 6 days ago by ▴ 30
0
votes
1
reply
177
views
homology modelling using swiss model
homology-modeling swiss-model
updated 5 days ago by 6.4k • written 6 days ago by • 0
0
votes
0
replies
81
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER MARINA ARACNe
5 days ago by Biostars2200 • 0
1
vote
5
replies
345
views
DYH17 Structure Prediction
BLAST Protein-Structure-Prediction
4 days ago by anasjamshed ▴ 120
0
votes
0
replies
132
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 5 days ago by 8.7k • written 6 days ago by • 0
3
votes
2
replies
276
views
p-value and Boneferroni adjusted p-value the same in R
Bonferroni R Statistics p-value Fisher
5 days ago by kristiewyleung • 0
2
votes
5
replies
457
views
Marking duplicates using UMIs
Deduplication UMI
updated 5 days ago by 19k • written 7 days ago by • 0
0
votes
0
replies
140
views
How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 6 days ago by 43k • written 7 days ago by • 0
0
votes
0
replies
141
views
Bacterial genome alignment with mauve
Bacteria mauve genome
7 days ago by rthapa ▴ 90
0
votes
0
replies
136
views
Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation CGenFF Gromacs VMD
7 days ago by Mamatha Y S • 0
0
votes
0
replies
132
views
News: upcoming online statistical courses
Statistics R Data-Analysis
updated 6 days ago by 43k • written 7 days ago by ★ 2.5k
0
votes
4
replies
530
views
how to find genes that are significantly expressed in brain cortex samples
rna-seq gene-expression
updated 7 days ago by 82k • written 8 days ago by ▴ 140
0
votes
2
replies
268
views
bam merging for archaic samples
samtools bam
updated 6 days ago by 43k • written 7 days ago by ▴ 100
7
votes
6
replies
484
views
Filtering sam or bam file with maximum matching region
crisper-edited alignment match
6 days ago by analyst ▴ 30
1
vote
1
reply
265
views
Removing Illumina microarray probes with no expression HumanHT-12v4
microarray HumanHT-12v4 Illumina
updated 7 days ago by ★ 7.0k • written 8 days ago by • 0
1
vote
0
replies
543
views
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Primers TRINITY
7 days ago by mathavanbioinfo ▴ 90
1
vote
1
reply
301
views
GTF file from Stringtie to R Studio for either Ballgown or DESeq2
Stringtie Cufflinks Ballgown DESeq2
updated 8 days ago by 43k • written 8 days ago by • 0
2
votes
5
replies
528
views
MEGA Analysis Issue on High-Performance Computer
phylogenetic-analysis MEGA
updated 7 days ago by ★ 27k • written 8 days ago by • 0
2
votes
1
reply
292
views
Running blastp with BLAST+ 2.15.0 against custom database; need to identify hits
shotgun metagenomics blastp taxonomy
updated 8 days ago by 141k • written 8 days ago by • 0
0
votes
0
replies
215
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools gcs
7 days ago by abhishekghadge • 0
2
votes
5
replies
695
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 7 days ago by ▴ 740 • written 8 days ago by ★ 2.4k
0
votes
0
replies
191
views
agilent microarray gpl data does not have gene symbol column
microarray agilent gpl
updated 8 days ago by 43k • written 8 days ago by • 0
0
votes
0
replies
190
views
scRNA Cluster frequency
CV PCA scRNA Cluster-Frequency
8 days ago by Nitin • 0
1
vote
5
replies
566
views
Duplicate marking, read names, and the SRA
SRA MarkDuplicates
updated 8 days ago by 141k • written 8 days ago by • 0
0
votes
0
replies
183
views
Chemical structure validation
structure cap validation metabolite
8 days ago by Rodolfo Adrián • 0
3
votes
8
replies
1.3k
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq Cellranger STARsolo 10X
updated 7 days ago by 14k • written 9 months ago by ▴ 80
0
votes
1
reply
266
views
Downloading the raw microarray data from GEO
.gpr microarray .CEL
updated 8 days ago by 141k • written 8 days ago by ▴ 10
0
votes
0
replies
208
views
Copy number variation plot
Copy-number-variation genomics
updated 8 days ago by 43k • written 8 days ago by • 0
1
vote
5
replies
708
views
RNA seq differential expression analysis
RNA-seq normalization
updated 8 days ago by ★ 1.7k • written 9 days ago by • 0
0
votes
0
replies
181
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs ngsTools ANGSD genomics
8 days ago by DanielEB_fisk ▴ 20
0
votes
1
reply
286
views
Could you please assist in identifying this cluster?
single-cell
updated 8 days ago by 43k • written 8 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
2
votes
7
replies
5.3k
views
6 follow
Memory usage of picard Samsort
Picard SortSam
updated 8 days ago by 82k • written 7.2 years ago by ▴ 80
5
votes
13
replies
1.2k
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R Ubuntu Linux Bioconductor Rstudio
updated 7 days ago by 82k • written 8 days ago by ★ 1.7k
1
vote
1
reply
419
views
Plink merge errors.
cygwin64 bed PLINK
8 days ago by Dinmukhamed • 0
0
votes
0
replies
200
views
Conversion to tree format
PLINK bed Figtree SplitsTree
updated 8 days ago by 43k • written 8 days ago by • 0
0
votes
0
replies
197
views
miRDeep2: How to get the read counts
mirdeep2
8 days ago by Atul K. • 0
3
votes
4
replies
666
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
5 days ago by rahu • 0
0
votes
0
replies
203
views
Lncipedia GTF file error
Proteomics
updated 8 days ago by 43k • written 8 days ago by ▴ 10
7
votes
3
replies
2.8k
views
Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation rRNA RNAmmer Genome
updated 9 days ago by 6.4k • written 15 months ago by ▴ 130
3
votes
3
replies
477
views
Free/open source 23andme-like analysis
SNPs genomics NGS VCF
updated 7 days ago by 14k • written 9 days ago by ▴ 520
0
votes
2
replies
542
views
How to get the reference panel for UKBB
UKBB GWAS clump
9 days ago by 航太郎 • 0
11
votes
12
replies
972
views
Downloaded pdb's on rcsb.org
rcsb pdb
updated 9 days ago by 43k • written 9 days ago by • 0
0
votes
0
replies
216
views
create genewise sync file in popoolation
popoolation
updated 9 days ago by 141k • written 9 days ago by • 0
0
votes
2
replies
379
views
error in coding potential calculator CPC2
cpc CPC2 coding-potential
9 days ago by Ashok • 0
0
votes
2
replies
416
views
miRNAs quantification using mirdeep2 tool
differential-expression mirdeep2 miRNA
9 days ago by Ashok • 0
116,634 results • Page 4 of 2333
Recent Votes
Comment: NGS forensics: how to know if data is fabricated
Comment: calculate nucleotide diversity from whole-genome-sequence data for individual ge
Comment: calculate nucleotide diversity from whole-genome-sequence data for individual ge
Answer: DNA methylation preprocessing
Comment: NGS forensics: how to know if data is fabricated
Answer: NGS forensics: how to know if data is fabricated
Comment: NGS forensics: how to know if data is fabricated
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Answer: How many reads for WGS Sequencing? by Mensur Dlakic ★ 27k
It takes 29 seconds to assemble this genome (20 CPUs) with the following statistics: 135 contigs, total 2821177 bp, min 200 bp, max …
Comment: NGS forensics: how to know if data is fabricated by noodle ▴ 520
IMO (and unfortunately) there needs to be an effort to develop these algorithms.
Comment: gvcf joint calling by Jeremy Leipzig 22k
the samples that are `./.` have no coverage (or not enough to call a genotype) and the `0/0` are homozygous reference
Answer: How many reads for WGS Sequencing? by GenoMax 141k
Did you download the complete dataset available from ENA/NCBI SRA? This is an older dataset (from 2012) with a total of 1146212 reads and 1…
Comment: When to use .vcf or .gvcf files from GATK HaplotypeCaller? by zihanss • 0
Hello, I want to know that why my gVCF files have "./." besides "0/0", "1/1"? Thanks
Comment: gvcf joint calling by zihanss • 0
![enter image description here][1] [1]: /media/images/15eedc1a-b2c6-4966-be39-b5173dab And I confused with the file that has "./." and…
Comment: gvcf joint calling by zihanss • 0
![enter image description here][1] [1]: /media/images/16fd502c-4e01-4f56-8562-0e0d4aac Okay, this is the merged gVCF file.
Comment: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC: by Mensur Dlakic ★ 27k
Enzymes under the umbrella of `1.1.1.-` work `with NAD(+) or NADP(+) as acceptor`. That only tells you about their cofactors, but not about…
Comment: NGS forensics: how to know if data is fabricated by dsull ★ 5.9k
I don't think people have undertaken the effort to create an anomaly detector for RNAseq -- people's efforts are dedicated towards developi…
Comment: NGS forensics: how to know if data is fabricated by dsull ★ 5.9k
I'd say post on pubpeer -- it's the best forum for this sort of discussion. As for what additional analysis I recommend: I'd say look at s…
Comment: NGS forensics: how to know if data is fabricated by noodle ▴ 520
> This is a super-interesting question from an algorithmic standpoint Ya, I was hoping to find some algorithm that would compare say a 're…
Comment: ScRNAseq-How to correctly choose cell type marker genes by Francesco ▴ 10
Thank you for your valuable suggestion!
Comment: NGS forensics: how to know if data is fabricated by noodle ▴ 520
> My first question would be how strong your background in such analysis > is. Very strong. PhD+several years working in the field. > Wot…
Comment: NGS forensics: how to know if data is fabricated by ATpoint 82k
My first question would be how strong your background in such analysis is. Claim of fabrication is very serious, so be 100% sure to back it…
Answer: NGS forensics: how to know if data is fabricated by Jeremy Leipzig 22k
This is a super-interesting question from an algorithmic standpoint (devising a model that can distinguish real from synthetic reads) but I…
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