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185 results • Page 1 of 4
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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 2 days ago by ★ 3.8k • written 10.8 years ago by ▴ 920
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 4 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 3 days ago by ▴ 850 • written 6.1 years ago by ▴ 10
8
votes
5
replies
5.4k
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 5 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 3 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 4 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 20 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 6 days ago by 10k • written 6.1 years ago by ▴ 10
0
votes
9
replies
2.4k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome nanopore basecalling fastq
updated 3 hours ago by • 0 • written 8 months ago by • 0
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 3 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 14 hours ago by 43k • written 8 months ago by ▴ 10
2
votes
3
replies
956
views
Method to detect genome doubling
CNV genome doubling
updated 6 days ago by 4.2k • written 4.5 years ago by ▴ 750
1
vote
10
replies
941
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq DESeq2 DNA-contamination
4 days ago by DKA ▴ 40
8
votes
16
replies
871
views
How to convert plink files to Hapmap Format
GWAS Plink
updated 2 days 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
813
views
AGeNT LocatIt
AGeNT LocatIt WES UMI duplicates
updated 4 days ago by ★ 2.1k • written 2.8 years ago by ▴ 10
1
vote
8
replies
806
views
Adding CB tag to bam file
samtools bam
updated 3 days ago by 161k • written 10 days ago by • 0
3
votes
3
replies
722
views
KissDE and batch effect
kissDE kissplice
6 days ago by david.b.rombaut ▴ 10
14
votes
10
replies
722
views
6 follow
NGS forensics: how to know if data is fabricated
fastq STAR NGS Illumina
updated 1 hour ago by ★ 27k • written 1 day ago by ▴ 530
0
votes
1
reply
688
views
Can I run cellassign on samples independently if there is batch effect present?
RNA-Seq R cellassign batch-effect
updated 11 hours ago by ▴ 10 • written 3.3 years ago by ▴ 30
4
votes
11
replies
685
views
Redirection of Duplicate PMIDs
pubmed pmid
updated 4 days ago by 4.2k • written 5 days ago by • 0
3
votes
4
replies
670
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
6 days ago by rahu • 0
3
votes
6
replies
662
views
Ciriquant not configuring hisat2 indexed files
ciriquant
6 days ago by Atul K. • 0
5
votes
4
replies
642
views
How to compare the quality of assemblies
nextdenovo assembly hifiasm pacbio
4 days ago by kirillkirilenko ▴ 40
4
votes
7
replies
610
views
7 follow
Heatmap and rna-seq
RNA-Seq Heatmap
updated 1 day ago by ★ 5.9k • written 5 days ago by ▴ 10
1
vote
5
replies
603
views
Cell barcode whitelists for DNBelab C Series High-throughput Single-cell RNA Series Library Preparation Set?
cell-barcode MGI DNBelab single-cell
updated 5 days ago by • 0 • written 3 months ago by • 0
0
votes
2
replies
589
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
8
votes
8
replies
584
views
PCA plot (Suggestions Needed)
DESeq2 PCAplot
updated 3 days ago by 14k • written 4 days ago by ▴ 10
3
votes
5
replies
556
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
4
votes
8
replies
549
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
520
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
497
views
python file for coding potential calculator
cpc2.py
updated 5 days ago by ▴ 10 • written 10 days ago by • 0
0
votes
1
reply
476
views
GAPIT p-value significance threshold
GAPIT p-value GWAS
updated 3 days ago by • 0 • written 4 months ago by • 0
3
votes
9
replies
463
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 4 days ago by 100k • written 6 days ago by • 0
4
votes
7
replies
460
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
2
votes
5
replies
459
views
Marking duplicates using UMIs
Deduplication UMI
updated 6 days ago by 19k • written 7 days ago by • 0
0
votes
6
replies
442
views
Use of Kraken output for functional analysis
metagenomics kraken shotgun
updated 4 days ago by • 0 • written 27 days ago by ▴ 20
2
votes
2
replies
432
views
Using vg gamsort with naive sorting algorithm
gamsort vg
updated 5 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
0
replies
409
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell Spatial-Transcriptomics
2 days ago by biocellbio • 0
1
vote
7
replies
402
views
gvcf joint calling
WES GATK VCF gVCF
14 hours ago by zihanss • 0
1
vote
6
replies
393
views
ScRNA data question
scRNA Vlnplot Samples
1 day ago by starswillfade ▴ 10
0
votes
3
replies
388
views
How to identify gaps in a genome?
awk seqkit assembly fasta genome
updated 5 days ago by 6.4k • written 13 days ago by • 0
4
votes
4
replies
388
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 1 day ago by ★ 1.7k • written 3 days ago by ★ 3.9k
185 results • Page 1 of 4
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Answer: NGS forensics: how to know if data is fabricated
Answer: NGS forensics: how to know if data is fabricated
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Answer: NGS forensics: how to know if data is fabricated
Comment: NGS forensics: how to know if data is fabricated
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Recent Replies
Comment: PDB related issue by Mensur Dlakic ★ 27k
The best way to find out is to read the original paper. My guess is that the residue has been crystallized in alternative conformations, wh…
Answer: NGS forensics: how to know if data is fabricated by Mensur Dlakic ★ 27k
I share the opinion by @philippbayer I have seen enough questionable things in life and in science to keep me permanently jaded, but there…
Comment: How many reads for WGS Sequencing? by Mensur Dlakic ★ 27k
I downloaded the data in two files from the link you provided. With this command: megahit -1 ERR072246_1.fastq.gz -2 ERR072246_2.fastq…
Comment: How many reads for WGS Sequencing? by Mensur Dlakic ★ 27k
If you have Linux the assembly should work on your system, but 8 GB is generally not enough for assembling larger genomes.
Comment: How many reads for WGS Sequencing? by Mensur Dlakic ★ 27k
I think you might be getting stuck on less relevant parts of my exercise. The most important point was that nothing is wrong with the data.…
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) …
Comment: 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…
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