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545 results • Page
3 of 11
Sort: Views
Rank
Views
Votes
Replies
1
vote
1
reply
815
views
Question for 3 prime bias in rna short read and long read (illumina, ont, pacbio)
rna-seq
short-read
long-read
updated 18 days ago by
Ram
43k • written 11 months ago by
shinyjj
▴ 50
0
votes
1
reply
815
views
Bulk RNAseq MACS Sort Quality Contamination
EdgeR
Batch-effect
RNA-Seq
updated 5 days ago by
Ram
43k • written 3.7 years ago by
jordan15
• 0
2
votes
10
replies
813
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated 26 days ago by
Ram
43k • written 9 weeks ago by
Sky
▴ 10
1
vote
2
replies
805
views
What type of normalization does removeBatchEffect function require as the input?
batch
limma
removeBatchEffect
rna-seq
batch-effect
updated 7 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
1
vote
4
replies
803
views
I want to calculate if the sample has whole genome duplication event or not?
sequencing
wgs
14 days ago by
Hyper_Odin
▴ 310
2
votes
7
replies
799
views
Removing duplicates
duplicates
ONT
minimap2
updated 5 days ago by
joe
▴ 510 • written 6 days ago by
quentinperriere
• 0
0
votes
1
reply
772
views
Error in genetics vcf file - !! Error (genfile::MalformedInputError): Source "file-path/data_chrxx.vcf.gz" is malformed on line 5145934..
vcf
genetics
updated 29 days ago by
m.medinagomez
• 0 • written 2.4 years ago by
Nance
• 0
0
votes
1
reply
744
views
Low SNP Overlap with Michigan 1KG and TopMed reference panel
Michigan-Server
Phasing
TopMed
updated 21 days ago by
Ram
43k • written 11 months ago by
berndmann
▴ 10
0
votes
0
replies
730
views
"No group or design set" with deAna() function in EnrichmentBrowser package
RNA-Seq
R
EnrichmentBrowser
updated 6 days ago by
Ram
43k • written 4.1 years ago by
yxswhx
• 0
0
votes
0
replies
729
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
RNA-Seq
scRNA-Seq
batch-effect
updated 5 days ago by
Ram
43k • written 3.4 years ago by
hkarakurt
▴ 180
2
votes
9
replies
723
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 4 hours ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
2
votes
12
replies
719
views
Nanopore data filtering using fastp
fastp
nanopore
26 days ago by
emilydolivo97
▴ 10
0
votes
3
replies
699
views
PCR duplicates in FFPE RNASeq
PCR-duplicates
RNA-Seq
FFPE
Variant-Calling
updated 28 days ago by
Ram
43k • written 22 months ago by
Gama313
▴ 120
8
votes
10
replies
688
views
bash script
whole-genome-sequencing
updated 8 days ago by
Ram
43k • written 15 days ago by
bestone
▴ 30
1
vote
0
replies
670
views
Conditions for valid batch effect correction
r
batch-effect
updated 7 days ago by
Ram
43k • written 5.2 years ago by
Sebastian Hesse
▴ 340
2
votes
5
replies
668
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 3 days ago by
Jesse
▴ 740 • written 4 days ago by
Ann
★ 2.4k
2
votes
5
replies
665
views
samtools mpileup taking too long
Bam
samtools
sam
alignment
updated 18 days ago by
Ram
43k • written 5 weeks ago by
K
• 0
1
vote
1
reply
656
views
Save experiment with batch effects - Protein microarray
statistics
protein-array
batch-effect
updated 7 days ago by
Ram
43k • written 4.4 years ago by
s.lima.diogenes
▴ 10
0
votes
1
reply
655
views
How to fix FreeBayes error "unable to find FASTA index entry for bed files"
freebayes
variant-calling
RNA-Seq
updated 21 days ago by
Ram
43k • written 13 months ago by
wlei091226
• 0
0
votes
1
reply
654
views
How to find the co ordinates of long reads (simulated by Badreads) with respect to the reference genome
long-reads
reference-genome
assembly
updated 18 days ago by
Ram
43k • written 2.7 years ago by
Ashi
▴ 20
0
votes
0
replies
649
views
METAL GWAS
allele-frequency
gwas
updated 21 days ago by
Ram
43k • written 2.4 years ago by
晗颖
• 0
2
votes
2
replies
625
views
Batch correction for DE analysis
batch-correction
mRNA
RNA-seq
DEGs
MDSplot
updated 7 days ago by
Ram
43k • written 2.6 years ago by
Yoonji
▴ 10
2
votes
6
replies
625
views
Overlapping and merging ChIP-seq peaks
MACS2
HOMER
ChIP-seq
peak-calling
updated 21 days ago by
Ram
43k • written 4 months ago by
zea
• 0
1
vote
2
replies
622
views
Nanopore multisample variant calling
SNPs
nanopore
SNP-calling
variants
multisample
25 days ago by
colindaven
6.4k
0
votes
0
replies
619
views
I performed Homer's annotatePeaks.pl on multiple tissues, yet when I run annotatePeaks on the merged tissues, I get fewer total annotated peaks. Is t…
Homer
ATACseq
24 days ago by
Ronin
• 0
0
votes
2
replies
612
views
Seeking Alternative Tools for Predicting Mature microRNAs from Vertebrate Animal Precursors in In Silico Study
mirdeep2
maturebayes
microrna
updated 21 days ago by
Ram
43k • written 12 months ago by
Beatriz
• 0
0
votes
6
replies
610
views
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data?
differential-expression
RNA-Seq
ONT
Nanopore
updated 14 days ago by
Ram
43k • written 4 months ago by
tw_140
• 0
0
votes
3
replies
606
views
Not all variants are annotated with AF - expected or a problem?
Variant-Calling
WGS
Alignment
updated 21 days ago by
Ram
43k • written 7 months ago by
Luiz
▴ 30
0
votes
10
replies
606
views
Nextflow ERROR : Timeout waiting for connection from pool
nextflow
22 days ago by
dzisis1986
▴ 70
1
vote
1
reply
596
views
accessing the global gut microbial gene catalogue (MEDUSA)
medusa
gene-catalogue
gut-microbiome
updated 12 days ago by
Ram
43k • written 3.2 years ago by
ramin.k2013
• 0
0
votes
0
replies
590
views
Avoid genome circularization with Canu assembler
circularization
ONT
Canu
repetitive-regions
assembler
updated 18 days ago by
Ram
43k • written 2.9 years ago by
Maria
• 0
0
votes
2
replies
576
views
Bacterial contamination in human DNA sample
Long-read-sequencing
Bacterial-contamination
updated 18 days ago by
Ram
43k • written 22 months ago by
priya.bmg
▴ 60
0
votes
3
replies
572
views
FindAllMarkers not working (Error (data layers are not joined. Please run JoinLayersWarning: When testing 1 versus all)
FindAllMarkers
seurat
re-clustering
26 days ago by
Nitin
• 0
0
votes
9
replies
571
views
99.9999% of Q30 bases is normal?
RNA-seq
fastp
updated 12 days ago by
LauferVA
4.2k • written 13 days ago by
Aki
▴ 10
0
votes
4
replies
569
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
4 days ago by
Kai Xin
• 0
4
votes
9
replies
561
views
variant calling
variant-calling
updated 20 days ago by
Ram
43k • written 21 days ago by
dalibenam64
• 0
4
votes
7
replies
554
views
Can any JBrowse2 tracks show multiple colors for reads at different nucleotide positions?
JBrowse
JBrowse2
updated 22 days ago by
cmdcolin
★ 3.8k • written 25 days ago by
I0110
▴ 140
0
votes
1
reply
549
views
Differential Expression Analysis for miRNA
limma
Differential-gene-Expression
miRNA
updated 14 days ago by
Ram
43k • written 2.9 years ago by
Al
• 0
1
vote
1
reply
538
views
GEO analysis with R
R
updated 21 days ago by
Ram
43k • written 2.3 years ago by
abdalla.m
• 0
0
votes
6
replies
536
views
PacBio adapters in transcriptome assembly from short read data?
adapter
transcriptome
sequencing
pacbio
vecscreen
8 days ago by
Dunois
★ 2.5k
4
votes
7
replies
535
views
DESeq2 Multifactor Design
RNA-seq
DESeq2
updated 10 days ago by
Ram
43k • written 11 days ago by
AHerik
▴ 20
0
votes
2
replies
534
views
autodockvina
python
python3
autodock
updated 5 days ago by
Ram
43k • written 3 months ago by
iamsmor
• 0
1
vote
0
replies
531
views
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Primers
TRINITY
3 days ago by
mathavanbioinfo
▴ 90
0
votes
2
replies
528
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
5 days ago by
航太郎
• 0
2
votes
6
replies
524
views
Need help understanding core SNPs
SNPs
snippy
29 days ago by
ujichu
• 0
0
votes
5
replies
517
views
seg fault, core dumped with manta 1.6.0
manta
gdb
updated 15 days ago by
Ram
43k • written 19 days ago by
Greg
• 0
0
votes
8
replies
515
views
STAR aligner options
STAR
26 days ago by
theophile
• 0
0
votes
1
reply
513
views
Geneious vs Perl script of IN SILICO PCR
PCR
Geneious
updated 21 days ago by
Ram
43k • written 23 months ago by
Bio_Crap
• 0
0
votes
2
replies
511
views
Gene expression assay Yeast sample prep
Live-cells
updated 21 days ago by
Ram
43k • written 22 months ago by
dshdixit
▴ 10
0
votes
4
replies
487
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
5 days ago by
feather-W
• 0
545 results • Page
3 of 11
Recent Votes
Comment: Per base sequence content error in RNAseq analysis
Answer: Gene set enrichment analysis differences between 2020 and 2024
Answer: Gene set enrichment analysis differences between 2020 and 2024
Answer: Gene set enrichment analysis differences between 2020 and 2024
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
Comment: TCGA2STAT Error: Firehose connection
Answer: HaplotypeCaller - only SNPs
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Recent Replies
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
by
Istvan Albert
100k
What I mean is that no sequencing run can be calibrated with the claimed precision. Where it could correctly distinguish between basecalls …
Comment: HaplotypeCaller - only SNPs
by
analyst
▴ 20
After HaplotypeCaller, you can use gatk SelectVariants to extract snps or indels from vcf file ([link to command][1]) [1]: https://gatk…
Comment: GTF file for Rhinolophus sinicus
by
atowns21
• 0
Ah gotcha. I guess what doesn't make sense to me is why a [paper][1] published in 2022 uses that reference genome. [1]: https://www.na…
Answer: Wilcox test using data slot (log normalized count values) of scRNA-seq between t
by
yxwucq
• 0
The best way is to generate a pseudo-bulk aggregation then apply edgeR or DESeq2. You can also directly use wilcoxon on sc-level, since man…
Comment: How to solve this RoseTTAFold colaboratory error?
by
Mensur Dlakic
★ 27k
There is a dedicated Discord group that deals with everything related to ColabFold and its derivatives. Below is an invitation to join that…
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie
by
atowns21
• 0
Hmm, okay I'm not sure what is going on, but here is what I did: 1. Downloaded a single fastq: `parallel-fastq-dump --tmpdir . --threads …
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
by
HyperEvo
• 0
Ok, thank you so much~
Comment: GTF file for Rhinolophus sinicus
by
GenoMax
141k
I was able to get the GTF file. I tried the fasta genome and it seemed to work but I did not complete the download. If you choose to ignore…
Comment: some error in building kraken2 database
by
Art1ess
• 0
I have 2 files output, no error logs... the .kreport file: 100.00 160136511 160136511 U 0 unclassified head .res…
Comment: TCGA2STAT Error: Firehose connection
by
LauferVA
4.2k
agree. from a data-centric (rather than software centric) standpoint, it shouldn't be hard to get the TCGA data you are looking for from o…
Comment: Redirection of Duplicate PMIDs
by
LauferVA
4.2k
yep. in this case id definitely start with the grant numbers themselves as others have indicated. i did not recommend this before due to un…
Comment: GTF file for Rhinolophus sinicus
by
atowns21
• 0
This download doesn't seem to work for me. There is a message on the website saying "Warning: contaminated. Status: RefSeq GCF_001888835.1 …
Answer: HaplotypeCaller - only SNPs
by
Pierre Lindenbaum
161k
Filter the vcf dowstream after haplotypecaller using bcftools or gatk variantfiltration
Answer: Gene set enrichment analysis differences between 2020 and 2024
by
geneontologyhelp
▴ 380
We have releases about monthly in order to keep our data accurate and reflect current understanding. In 4 years, there have been about 40 r…
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie
by
GenoMax
141k
Let us know when you find out. Would be a useful thing to know what the data looks like.
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