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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
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
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
12
replies
313
views
How many reads for WGS Sequencing?
WGS Bacterial-Genomics
updated 56 minutes ago by ★ 27k • written 18 hours ago by • 0
4
votes
11
replies
680
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 5 days ago by 43k • written 14.6 years ago by 100k
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
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
1
vote
10
replies
938
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq DESeq2 DNA-contamination
4 days ago by DKA ▴ 40
13
votes
10
replies
699
views
6 follow
NGS forensics: how to know if data is fabricated
fastq STAR NGS Illumina
updated 38 minutes ago by ★ 27k • written 1 day ago by ▴ 530
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
9
replies
2.4k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome nanopore basecalling fastq
updated 2 hours ago by • 0 • written 8 months ago by • 0
3
votes
9
replies
462
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
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
0
votes
8
replies
335
views
Error in cnetplot enrichplot package
R
updated 6 days ago by 43k • written 6 days ago by • 0
4
votes
8
replies
546
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
8
votes
8
replies
583
views
PCA plot (Suggestions Needed)
DESeq2 PCAplot
updated 3 days ago by 14k • written 4 days ago by ▴ 10
1
vote
7
replies
395
views
gvcf joint calling
WES GATK VCF gVCF
13 hours ago by zihanss • 0
4
votes
7
replies
459
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
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
0
votes
7
replies
328
views
Low mapping rate with Salmon
RNA-seq Salmon Quantification
updated 2 days ago by 141k • written 6 days ago by • 0
4
votes
7
replies
608
views
7 follow
Heatmap and rna-seq
RNA-Seq Heatmap
updated 1 day ago by ★ 5.9k • written 5 days ago by ▴ 10
2
votes
6
replies
1.1k
views
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq Salmon Isoseq
updated 13 hours ago by 43k • written 8 months ago by ▴ 10
1
vote
6
replies
391
views
ScRNA data question
scRNA Vlnplot Samples
1 day 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
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
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
0
votes
6
replies
326
views
How to slice a gvcf file with tabix?
Tabix bed gvcf
5 days ago by Sd • 0
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
3
votes
6
replies
661
views
Ciriquant not configuring hisat2 indexed files
ciriquant
6 days ago by Atul K. • 0
0
votes
5
replies
330
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative ncbi asembly refseq
updated 3 days ago by 141k • written 4 days ago by ▴ 90
1
vote
5
replies
284
views
Downsampling fastq file
downsample fastq
updated 6 days ago by 43k • written 6 days ago by ▴ 80
0
votes
5
replies
324
views
different FeatureCounts output for the same data
fpkm Counts Rsubread rna-seq
updated 1 day ago by 100k • written 4 days ago by ▴ 10
8
votes
5
replies
5.4k
views
ISCN annotation for SV/CN VCF files
SV
written 7 months ago by ▴ 60
2
votes
5
replies
458
views
Marking duplicates using UMIs
Deduplication UMI
updated 6 days ago by 19k • written 7 days ago by • 0
2
votes
5
replies
343
views
Fetch table from clinvar database according to a list of rsid
python clinvar perl
3 hours ago by ashaneev07 ▴ 20
2
votes
5
replies
306
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq assembly transcriptome contamination
2 days ago by Lada ▴ 30
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
3
votes
5
replies
279
views
Per base sequence content error in RNAseq analysis
RNA-seq analysis
updated 6 days ago by 141k • written 6 days ago by • 0
0
votes
5
replies
320
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap alignment minimap2 GRCh38 assembly
4 days ago by njornet ▴ 20
1
vote
5
replies
350
views
DYH17 Structure Prediction
BLAST Protein-Structure-Prediction
5 days ago by anasjamshed ▴ 120
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
2
votes
4
replies
308
views
Should I use unpaired reads from trimmomatic
RNA-seq QC Trimmomatic
updated 4 days ago by 14k • written 6 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
4
votes
4
replies
387
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
2
votes
4
replies
285
views
interpretartion of a vcf file
calling genotype ONT variant diploid
4 days ago by samuelkalandarov2002 ▴ 10
5
votes
4
replies
642
views
How to compare the quality of assemblies
nextdenovo assembly hifiasm pacbio
4 days ago by kirillkirilenko ▴ 40
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
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
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
185 results • Page 1 of 4
Recent Votes
Answer: NGS forensics: how to know if data is fabricated
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
Comment: NGS forensics: how to know if data is fabricated
Answer: How to use limma to find differentially expressed genes in response to a continu
Batch effects : ComBat or removebatcheffects (limma package) ?
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Recent Replies
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…
Comment: How many reads for WGS Sequencing? by GenoMax 141k
> What does clipped Fastq mean? Probably means that NCBI has already scanned and trimmed adapter sequencers. > both forward and revers…
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