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76
votes
72
replies
19k
views
19 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
3 days ago by Kevin Blighe 87k
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 1 day ago by ★ 3.8k • written 10.8 years ago by ▴ 920
2
votes
5
replies
10k
views
Find Corresponding Author: Doi Metadata?
updated 6 days ago by 43k • written 10.6 years ago by ▴ 150
10
votes
6
replies
9.9k
views
6 follow
CDS vs cDNA vs transcript for mapping RNA-Seq reads
Assembly rna-seq alignment
updated 2 days ago by ★ 5.1k • written 6.0 years ago by ▴ 510
14
votes
2
replies
7.0k
views
Trouble with Pilon installation
polishing pilon installation
updated 3 days ago by • 0 • written 7.3 years ago by ★ 1.4k
7
votes
7
replies
5.9k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq SNP
updated 2 days ago by ▴ 850 • written 6.1 years ago by ▴ 10
8
votes
5
replies
5.3k
views
ISCN annotation for SV/CN VCF files
SV
written 7 months ago by ▴ 60
25
votes
11
replies
3.7k
views
6 follow
Forum: Site Use Guidelines
meta biostars Guidelines
updated 4 days ago by 43k • written 14.6 years ago by 100k
2
votes
6
replies
3.7k
views
Treatment VS Control in Single Cell RNAseq analysis
Single Cell RNAseq DE Analysis Treatment Control
updated 2 days ago by 82k • written 3.9 years ago by ▴ 280
0
votes
13
replies
3.5k
views
6 follow
Tax4Fun2 - error
tax4fun silva blast
updated 3 days ago by • 0 • written 2.2 years ago by ▴ 10
0
votes
4
replies
2.7k
views
Lositan freezing when generating selection table
LOSITAN
updated 3 days ago by • 0 • written 8.3 years ago by • 0
2
votes
3
replies
2.5k
views
When to use .vcf or .gvcf files from GATK HaplotypeCaller?
indel gatk calling snp variant
updated 8 hours ago by • 0 • written 23 months ago by ▴ 120
1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink PED
updated 5 days ago by 10k • written 6.1 years ago by ▴ 10
2
votes
4
replies
2.4k
views
How could I generate a gi_taxid_nucl.dmp file similar to the one previously hosted by NCBI?
ncbi metagenomics centrifuge gi_taxid_nucl.dmp taxonomy
updated 3 days ago by • 0 • written 2.4 years ago by • 0
3
votes
3
replies
2.3k
views
How to make a TSS enrichment plot in ATAC-seq analysis?
ATAC
updated 2 days ago by • 0 • written 22 months ago by ▴ 180
3
votes
6
replies
1.9k
views
7 follow
DNA methylation preprocessing
SWAN DNA methylation Funnorm
updated 1 day ago by 43k • written 2.4 years ago by ▴ 10
2
votes
6
replies
1.1k
views
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq Salmon Isoseq
updated 1 hour ago by 43k • written 8 months ago by ▴ 10
2
votes
3
replies
954
views
Method to detect genome doubling
CNV genome doubling
updated 5 days ago by 4.2k • written 4.5 years ago by ▴ 750
1
vote
10
replies
938
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq DESeq2 DNA-contamination
3 days ago by DKA ▴ 40
8
votes
16
replies
858
views
How to convert plink files to Hapmap Format
GWAS Plink
updated 1 day ago by ★ 2.4k • written 7 weeks ago by • 0
2
votes
9
replies
846
views
TCGA2STAT Error: Firehose connection
FIREHOSE TCGA
updated 4 days ago by 4.2k • written 6 months ago by • 0
0
votes
2
replies
810
views
AGeNT LocatIt
AGeNT LocatIt WES UMI duplicates
updated 3 days ago by ★ 2.1k • written 2.8 years ago by ▴ 10
1
vote
8
replies
805
views
Adding CB tag to bam file
samtools bam
updated 3 days ago by 161k • written 9 days ago by • 0
3
votes
3
replies
722
views
KissDE and batch effect
kissDE kissplice
5 days ago by david.b.rombaut ▴ 10
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
3
votes
6
replies
658
views
Ciriquant not configuring hisat2 indexed files
ciriquant
6 days ago by Atul K. • 0
5
votes
4
replies
637
views
How to compare the quality of assemblies
nextdenovo assembly hifiasm pacbio
4 days ago by kirillkirilenko ▴ 40
4
votes
11
replies
630
views
Redirection of Duplicate PMIDs
pubmed pmid
updated 4 days ago by 4.2k • written 5 days ago by • 0
1
vote
5
replies
602
views
Cell barcode whitelists for DNBelab C Series High-throughput Single-cell RNA Series Library Preparation Set?
cell-barcode MGI DNBelab single-cell
updated 4 days ago by • 0 • written 3 months ago by • 0
0
votes
2
replies
587
views
Why cd-hit-est not work when sequence identity threshold<0.95？
genome cluster sequence
updated 3 days ago by • 0 • written 21 months ago by • 0
4
votes
7
replies
578
views
7 follow
Heatmap and rna-seq
RNA-Seq Heatmap
updated 1 day ago by ★ 5.9k • written 5 days ago by ▴ 10
8
votes
8
replies
572
views
PCA plot (Suggestions Needed)
DESeq2 PCAplot
updated 3 days ago by 14k • written 4 days ago by ▴ 10
3
votes
5
replies
554
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align RNA-Seq linux STAR
6 days ago by n_navy • 0
7
votes
7
replies
537
views
NGS forensics: how to know if data is fabricated
fastq STAR NGS Illumina
5 hours ago by noodle ▴ 520
4
votes
8
replies
520
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs BED eqtl bedtools
updated 1 day ago by 35k • written 2 days ago by ▴ 10
0
votes
11
replies
512
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo scRNA-seq STAR snRNA-seq MGI
2 days ago by atowns21 • 0
0
votes
3
replies
494
views
python file for coding potential calculator
cpc2.py
updated 5 days ago by ▴ 10 • written 9 days ago by • 0
7
votes
6
replies
485
views
Filtering sam or bam file with maximum matching region
crisper-edited alignment match
6 days ago by analyst ▴ 30
0
votes
1
reply
460
views
GAPIT p-value significance threshold
GAPIT p-value GWAS
updated 2 days ago by • 0 • written 4 months ago by • 0
2
votes
5
replies
457
views
Marking duplicates using UMIs
Deduplication UMI
updated 6 days ago by 19k • written 7 days ago by • 0
3
votes
9
replies
454
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 3 days ago by 100k • written 5 days ago by • 0
4
votes
7
replies
450
views
To get p-values for the TPM
P-value TPM RSEM
updated 3 days ago by ★ 5.9k • written 4 days ago by • 0
0
votes
6
replies
438
views
Use of Kraken output for functional analysis
metagenomics kraken shotgun
updated 4 days ago by • 0 • written 26 days ago by ▴ 20
2
votes
2
replies
432
views
Using vg gamsort with naive sorting algorithm
gamsort vg
updated 4 days ago by 161k • written 8 months ago by ▴ 80
1
vote
4
replies
431
views
GTF file for Rhinolophus sinicus
Rhinolophus-sinicus GTF
updated 4 days ago by • 0 • written 5 months ago by • 0
0
votes
3
replies
384
views
How to identify gaps in a genome?
awk seqkit assembly fasta genome
updated 4 days ago by 6.4k • written 13 days ago by • 0
4
votes
4
replies
378
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 20 hours ago by ★ 1.7k • written 3 days ago by ★ 3.9k
4
votes
2
replies
375
views
Missing protein (VEGF-A) in String db
VGFA stringdb
updated 2 days ago by • 0 • written 11 weeks ago by ▴ 20
1
vote
6
replies
370
views
ScRNA data question
scRNA Vlnplot Samples
23 hours ago by starswillfade ▴ 10
1
vote
5
replies
345
views
DYH17 Structure Prediction
BLAST Protein-Structure-Prediction
4 days ago by anasjamshed ▴ 120
184 results • Page 1 of 4
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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
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Recent Replies
Comment: gvcf joint calling by zihanss • 0
Thanks for your comment, I get it now.
Answer: ChIP-seq datasets: input samples omitted? by ATpoint 82k
In my hands (and from what I know based on many years here) inputs are almost exclusively used during peak calling to correct for loci-spec…
Comment: How to assign cell types after integration in scRNA by ATpoint 82k
No difference here. After all you typically want a label per cluster/group, so either subset to the control condition to do the assignment,…
Comment: Differential Expression using Isoseq-supplemented reference transcriptome by gaoanwei • 0
I found the question and ASK the GPT4 turbo
Answer: Differential Expression using Isoseq-supplemented reference transcriptome by gaoanwei • 0
Your approach seems reasonable and well-informed, though it's perhaps less customary in the field, which could be why you haven't found pap…
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…
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