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182 results • Page
1 of 4
Sort: replies
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Views
Votes
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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
2 days ago by
Kevin Blighe
87k
8
votes
16
replies
838
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 1 day ago by
bk11
★ 2.4k • written 7 weeks ago by
Sofia
• 0
0
votes
13
replies
3.5k
views
6 follow
Tax4Fun2 - error
tax4fun
silva
blast
updated 3 days ago by
drstalinantony28
• 0 • written 2.2 years ago by
ymj
▴ 10
0
votes
11
replies
500
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
1 day ago by
atowns21
• 0
4
votes
11
replies
587
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 3 days ago by
LauferVA
4.2k • written 4 days ago by
dominickd
• 0
25
votes
11
replies
3.7k
views
6 follow
Forum:
Site Use Guidelines
meta
biostars
Guidelines
updated 4 days ago by
Ram
43k • written 14.6 years ago by
Istvan Albert
100k
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
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
1
vote
10
replies
930
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
3 days ago by
DKA
▴ 40
3
votes
9
replies
447
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 3 days ago by
Istvan Albert
100k • written 5 days ago by
Κοσμάς
• 0
2
votes
9
replies
841
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 3 days ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
8
votes
8
replies
564
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 2 days ago by
swbarnes2
14k • written 3 days ago by
Aaliya
▴ 10
0
votes
8
replies
330
views
Error in cnetplot enrichplot package
R
updated 5 days ago by
Ram
43k • written 5 days ago by
Farhad
• 0
4
votes
8
replies
496
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 19 hours ago by
Alex Reynolds
35k • written 1 day ago by
J
▴ 10
1
vote
8
replies
790
views
Adding CB tag to bam file
samtools
bam
updated 2 days ago by
Pierre Lindenbaum
161k • written 9 days ago by
Maria
• 0
4
votes
7
replies
553
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 17 hours ago by
dsull
★ 5.9k • written 4 days ago by
qudrat.nii
▴ 10
4
votes
7
replies
442
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 2 days ago by
dsull
★ 5.9k • written 3 days ago by
VITALA
• 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
rohitsatyam102
▴ 850 • written 6.1 years ago by
smallfish
▴ 10
0
votes
7
replies
316
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 1 day ago by
GenoMax
141k • written 5 days ago by
Patadu94
• 0
1
vote
6
replies
343
views
ScRNA data question
scRNA
Vlnplot
Samples
12 hours ago by
starswillfade
▴ 10
7
votes
6
replies
481
views
Filtering sam or bam file with maximum matching region
crisper-edited
alignment
match
6 days ago by
analyst
▴ 30
3
votes
6
replies
1.9k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 23 hours ago by
Ram
43k • written 2.4 years ago by
SYOSY
▴ 10
0
votes
6
replies
320
views
How to slice a gvcf file with tabix?
Tabix
bed
gvcf
4 days ago by
Sd
• 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
Antonio R. Franco
★ 5.1k • written 6.0 years ago by
williamsbrian5064
▴ 510
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
ATpoint
82k • written 3.9 years ago by
grayapply2009
▴ 280
0
votes
6
replies
436
views
Use of Kraken output for functional analysis
metagenomics
kraken
shotgun
updated 3 days ago by
gv
• 0 • written 26 days ago by
Srinka
▴ 20
6
votes
6
replies
283
views
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 39 minutes ago by
dsull
★ 5.9k • written 4 hours ago by
noodle
▴ 520
3
votes
6
replies
655
views
Ciriquant not configuring hisat2 indexed files
ciriquant
5 days ago by
Atul K.
• 0
3
votes
5
replies
553
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
5
replies
300
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 8 hours ago by
Istvan Albert
100k • written 3 days ago by
sehriban.buyukkilic
▴ 10
0
votes
5
replies
311
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
275
views
Per base sequence content error in RNAseq analysis
RNA-seq
analysis
updated 5 days ago by
GenoMax
141k • written 5 days ago by
ahmad.sajad4541
• 0
0
votes
5
replies
308
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
GenoMax
141k • written 3 days ago by
Bertalan_Takacs
▴ 90
2
votes
5
replies
10k
views
Find Corresponding Author: Doi Metadata?
updated 6 days ago by
Ram
43k • written 10.6 years ago by
Louis
▴ 150
1
vote
5
replies
599
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
atowns21
• 0 • written 3 months ago by
benjamin.pyenson
• 0
1
vote
5
replies
341
views
DYH17 Structure Prediction
BLAST
Protein-Structure-Prediction
4 days ago by
anasjamshed
▴ 120
2
votes
5
replies
293
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq
assembly
transcriptome
contamination
1 day ago by
Lada
▴ 30
2
votes
5
replies
457
views
Marking duplicates using UMIs
Deduplication
UMI
updated 5 days ago by
i.sudbery
19k • written 6 days ago by
Lipika
• 0
1
vote
5
replies
282
views
Downsampling fastq file
downsample
fastq
updated 5 days ago by
Ram
43k • written 5 days ago by
marco.barr
▴ 80
8
votes
5
replies
5.3k
views
ISCN annotation for SV/CN VCF files
SV
written 7 months ago by
a.beggs
▴ 60
4
votes
4
replies
369
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 9 hours ago by
BioinfGuru
★ 1.7k • written 2 days ago by
Ming Tommy Tang
★ 3.9k
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
ZhangYuanfeng
• 0 • written 2.4 years ago by
Frazier Baker
• 0
2
votes
4
replies
316
views
What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
ChIP-seq
3 days ago by
HyperEvo
• 0
2
votes
4
replies
293
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
updated 2 days ago by
Ram
43k • written 2 days ago by
ashaneev07
▴ 20
5
votes
4
replies
635
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
3 days ago by
kirillkirilenko
▴ 40
2
votes
4
replies
305
views
Should I use unpaired reads from trimmomatic
RNA-seq
QC
Trimmomatic
updated 4 days ago by
swbarnes2
14k • written 5 days ago by
dxj294
• 0
1
vote
4
replies
427
views
GTF file for Rhinolophus sinicus
Rhinolophus-sinicus
GTF
updated 3 days ago by
atowns21
• 0 • written 5 months ago by
ara
• 0
2
votes
4
replies
279
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
3 days ago by
samuelkalandarov2002
▴ 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
0
votes
4
replies
2.7k
views
Lositan freezing when generating selection table
LOSITAN
updated 2 days ago by
evawillms183
• 0 • written 8.3 years ago by
andrepleao
• 0
3
votes
4
replies
280
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
2 days ago by
QX
• 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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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
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Jesse
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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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Arup Ghosh
3.2k
Use the standalone version of Nextflow and specify the process-specific conda environments paths.
Comment: gvcf joint calling
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Jeremy Leipzig
22k
can you show us an exonic position in your VCF file that is all `./.`?
Comment: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
by
O.rka
▴ 710
Thank you. This answers my question. The reason I am asking is because I’m trying to do set enrichment analysis with BRENDA pathways using…
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
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6.4k
I used to use nextflow in a conda env. That requires the env to be active when a pipeline is started. Also I have productive pipelines whic…
Comment: different FeatureCounts output for the same data
by
Istvan Albert
100k
just to clarify, it is not that the program algorithm works differently but the meaning of the flags changed; before -p was sufficient to…
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
BioinfGuru
★ 1.7k
Thanks Ram. Using merge maxed out my ram on a large list, but your suggestion directed me to purrr::reduce which works great.
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