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182 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
8
votes
16
replies
851
views
How to convert plink files to Hapmap Format
GWAS Plink
updated 1 day ago by ★ 2.4k • written 7 weeks ago by • 0
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
11
replies
508
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
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
4
votes
11
replies
606
views
Redirection of Duplicate PMIDs
pubmed pmid
updated 4 days ago by 4.2k • written 5 days ago by • 0
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
1
vote
10
replies
933
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq DESeq2 DNA-contamination
3 days ago by DKA ▴ 40
3
votes
9
replies
452
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
2
votes
9
replies
842
views
TCGA2STAT Error: Firehose connection
FIREHOSE TCGA
updated 4 days ago by 4.2k • written 6 months ago by • 0
1
vote
8
replies
795
views
Adding CB tag to bam file
samtools bam
updated 2 days ago by 161k • written 9 days ago by • 0
8
votes
8
replies
566
views
PCA plot (Suggestions Needed)
DESeq2 PCAplot
updated 2 days ago by 14k • written 3 days ago by ▴ 10
4
votes
8
replies
505
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 1 day ago by ▴ 10
0
votes
8
replies
331
views
Error in cnetplot enrichplot package
R
updated 5 days ago by 43k • written 5 days ago by • 0
4
votes
7
replies
563
views
7 follow
Heatmap and rna-seq
RNA-Seq Heatmap
updated 21 hours ago by ★ 5.9k • written 4 days ago by ▴ 10
4
votes
7
replies
445
views
To get p-values for the TPM
P-value TPM RSEM
updated 2 days ago by ★ 5.9k • written 3 days ago by • 0
0
votes
7
replies
323
views
Low mapping rate with Salmon
RNA-seq Salmon Quantification
updated 1 day ago by 141k • written 5 days ago by • 0
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
2
votes
6
replies
3.6k
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
1
vote
6
replies
354
views
ScRNA data question
scRNA Vlnplot Samples
16 hours ago by starswillfade ▴ 10
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
3
votes
6
replies
656
views
Ciriquant not configuring hisat2 indexed files
ciriquant
5 days ago by Atul K. • 0
10
votes
6
replies
9.9k
views
6 follow
CDS vs cDNA vs transcript for mapping RNA-Seq reads
Assembly rna-seq alignment
updated 1 day ago by ★ 5.1k • written 6.0 years ago by ▴ 510
7
votes
6
replies
482
views
Filtering sam or bam file with maximum matching region
crisper-edited alignment match
6 days ago by analyst ▴ 30
1
vote
6
replies
247
views
gvcf joint calling
WES GATK VCF gVCF
updated 20 minutes ago by 22k • written 1 day ago by • 0
0
votes
6
replies
437
views
Use of Kraken output for functional analysis
metagenomics kraken shotgun
updated 3 days ago by • 0 • written 26 days ago by ▴ 20
0
votes
6
replies
320
views
How to slice a gvcf file with tabix?
Tabix bed gvcf
4 days ago by Sd • 0
6
votes
6
replies
377
views
NGS forensics: how to know if data is fabricated
fastq STAR NGS Illumina
updated 5 hours ago by ★ 5.9k • written 8 hours ago by ▴ 520
0
votes
5
replies
316
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap alignment minimap2 GRCh38 assembly
3 days ago by njornet ▴ 20
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
3
votes
5
replies
275
views
Per base sequence content error in RNAseq analysis
RNA-seq analysis
updated 5 days ago by 141k • written 5 days ago by • 0
0
votes
5
replies
311
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative ncbi asembly refseq
updated 2 days ago by 141k • written 3 days ago by ▴ 90
0
votes
5
replies
306
views
different FeatureCounts output for the same data
fpkm Counts Rsubread rna-seq
updated 13 hours ago by 100k • written 3 days ago by ▴ 10
1
vote
5
replies
600
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
2
votes
5
replies
296
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq assembly transcriptome contamination
1 day ago by Lada ▴ 30
1
vote
5
replies
344
views
DYH17 Structure Prediction
BLAST Protein-Structure-Prediction
4 days ago by anasjamshed ▴ 120
8
votes
5
replies
5.3k
views
ISCN annotation for SV/CN VCF files
SV
written 7 months ago by ▴ 60
1
vote
5
replies
282
views
Downsampling fastq file
downsample fastq
updated 5 days ago by 43k • written 5 days ago by ▴ 80
2
votes
5
replies
457
views
Marking duplicates using UMIs
Deduplication UMI
updated 5 days ago by 19k • written 7 days ago by • 0
2
votes
5
replies
10k
views
Find Corresponding Author: Doi Metadata?
updated 6 days ago by 43k • written 10.6 years ago by ▴ 150
4
votes
4
replies
375
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 14 hours ago by ★ 1.7k • written 3 days ago by ★ 3.9k
2
votes
4
replies
279
views
interpretartion of a vcf file
calling genotype ONT variant diploid
3 days ago by samuelkalandarov2002 ▴ 10
2
votes
4
replies
299
views
Fetch table from clinvar database according to a list of rsid
python clinvar perl
updated 2 days ago by 43k • written 2 days ago by ▴ 20
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 2 days ago by • 0 • written 2.4 years ago by • 0
2
votes
4
replies
317
views
What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
ChIP-seq
4 days ago by HyperEvo • 0
1
vote
4
replies
428
views
GTF file for Rhinolophus sinicus
Rhinolophus-sinicus GTF
updated 3 days ago by • 0 • written 5 months ago by • 0
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
5
votes
4
replies
636
views
How to compare the quality of assemblies
nextdenovo assembly hifiasm pacbio
3 days ago by kirillkirilenko ▴ 40
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
2
votes
4
replies
306
views
Should I use unpaired reads from trimmomatic
RNA-seq QC Trimmomatic
updated 4 days ago by 14k • written 5 days ago by • 0
182 results • Page 1 of 4
Recent Votes
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
correcting for a batch in DESeq2
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Recent Replies
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…
Answer: absolute path for symbolic links in Snakefile by Jesse ▴ 740
It's nothing to do with Snakemake, just the ordinary confusion of making relative symlinks when your working directory is somewhere else. …
Answer: Hide positions in alignment with 99% "–" characters to ignore single sequence in by Jesse ▴ 740
[seqmagick](https://github.com/fhcrc/seqmagick/) has a `--squeeze-threshold` option that does just this. For example with an MSA of five s…
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