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326 results • Page
4 of 7
Sort: Rank
Rank
Views
Votes
Replies
1
vote
1
reply
267
views
Inconsistency in SNP detection pipelines for multi-sample analysis
vcf
bam
bcf
snps
updated 6 days ago by
LChart
3.9k • written 6 days ago by
George
▴ 10
0
votes
4
replies
568
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
4 days ago by
Kai Xin
• 0
1
vote
1
reply
218
views
Retrieve a % coverage for each transcript
RNA-seq
updated 6 days ago by
Ram
43k • written 6 days ago by
jammydodger123456
▴ 40
0
votes
1
reply
334
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics
bootstrap
updated 6 days ago by
Klaus S
▴ 150 • written 11 days ago by
Zeng Hao
▴ 40
0
votes
2
replies
361
views
How can I solve this error?
metal
6 days ago by
22211020193
• 0
0
votes
0
replies
161
views
Struggling to lift genome builds
PLINK
liftover
GWAS
updated 6 days ago by
GenoMax
141k • written 6 days ago by
srimmer
• 0
1
vote
2
replies
266
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 6 days ago by
Ram
43k • written 6 days ago by
aniigodwinn
• 0
2
votes
3
replies
401
views
Sheep reference genome remapping coordinates
reference
remap
sheep
coordinates
genome
5 days ago by
valentinatsar
• 0
2
votes
3
replies
293
views
Editing Human Reference Genome by adding a CDS
gff
agat
transcriptome
updated 6 days ago by
Michael
54k • written 6 days ago by
LDT
▴ 340
2
votes
10
replies
717
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 5 days ago by
GenoMax
141k • written 6 days ago by
me
• 0
2
votes
2
replies
367
views
differential gene expression analysis when not all samples have an untreated counterpart
differential-expression
edgeR
5 days ago by
nhaus
▴ 300
0
votes
0
replies
349
views
Looking for an explanation as to what the Peak Score is from HOMER, not finding any answers on Biostars yet
Homer
ATAC-seq
6 days ago by
Ronin
• 0
4
votes
2
replies
1.7k
views
How to convert SAM/BAM file to GTF/GFF file?
GTF
SAM
BAM
GFF
minimap2
updated 6 days ago by
Dr.Animo
▴ 130 • written 12 months ago by
BioinfoBee
• 0
2
votes
7
replies
798
views
Removing duplicates
duplicates
ONT
minimap2
updated 5 days ago by
joe
▴ 510 • written 6 days ago by
quentinperriere
• 0
0
votes
1
reply
191
views
Annotating a dataset with gnomAD v4 using Hail
Python
Sequencing
Hail
Exome
Annotation
updated 6 days ago by
DKA
▴ 40 • written 6 days ago by
james.melhorn
• 0
3
votes
4
replies
416
views
biomaRt error for different R version
biomaRt
R
updated 5 days ago by
GenoMax
141k • written 6 days ago by
manaswwm
▴ 490
0
votes
1
reply
178
views
Freyja plot error
Freyja
updated 6 days ago by
Ram
43k • written 6 days ago by
Adyasha
• 0
1
vote
2
replies
192
views
Interpretation of combined P values - RNA microarray meta analysis
metaanalysis
R
microarray
DExMA
combinedP
6 days ago by
hagl
▴ 10
0
votes
0
replies
152
views
BIOM format can contain tabular data ?
BIOM
phyloseq
biomformat
R
6 days ago by
chemokine-1
▴ 10
0
votes
4
replies
487
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
5 days ago by
feather-W
• 0
0
votes
0
replies
224
views
Job:
Consultant to update a Snakemake workflow with the new Kubernetes executor plugin for Snakemake 8
Kubernetes
DevOps
executor
AWS
Snakemake
updated 6 days ago by
Michael
54k • written 6 days ago by
jonrkarr
▴ 100
0
votes
2
replies
210
views
Bedmethyl file format
bedmethyl
methylation
updated 6 days ago by
GenoMax
141k • written 6 days ago by
njornet
▴ 20
0
votes
0
replies
165
views
sequence table for DADA2 chimera filtering
OTU
sequencetable
DADA2
6 days ago by
Ali
• 0
2
votes
4
replies
304
views
SnpEff annotates coding duplication as intronic?
snpeff
6 days ago by
kirill.zaslavsky
• 0
0
votes
2
replies
236
views
Calculating percentage of cells proliferating in single cell rna seq data
statistics
scRNA-seq
proliferation
6 days ago by
mropri
▴ 150
0
votes
0
replies
179
views
Job:
Ensembl Outreach Project Leader
ebi
embl
genomics
ensembl
1 day ago by
Ben_Ensembl
★ 2.4k
0
votes
2
replies
304
views
GSEA analysis in R
GSEA
R
Arabidopsis
5 days ago by
Sudip
• 0
0
votes
2
replies
362
views
Which experiments generate Position Frequency Matrix?
Position-Frequency-Matrix
6 days ago by
arriyaz.nstu
▴ 30
2
votes
5
replies
420
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats
hg002
bed
homopolymer-regions
6 days ago by
Bikram Kumar
• 0
6
votes
8
replies
528
views
BRAKER3 genome annotation
annotation
BRAKER3
genome
updated 6 days ago by
dariober
14k • written 8 days ago by
manaswiniparija3
▴ 40
0
votes
2
replies
230
views
VCF annotation with gnomADv4 using R package
annotation
gnomADv4
R
VCF
6 days ago by
DKA
▴ 40
87
votes
24
replies
23k
views
17 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 6 days ago by
Gordon
• 0 • written 3.5 years ago by
Hamid Ghaedi
3.2k
3
votes
6
replies
613
views
Ciriquant not configuring hisat2 indexed files
ciriquant
1 day ago by
Atul K.
• 0
1
vote
2
replies
327
views
Forum:
VCF bulk handling
bcftools
SnpEff
WGS
VEP
VCF
6 days ago by
Javier
• 0
1
vote
3
replies
287
views
Merging vcf files with bcftools ([E::get_intv] Failed to parse TBX_VCF, was wrong -p [type] used?)
vcf
tabix
bcftools
updated 6 days ago by
Pierre Lindenbaum
161k • written 12 days ago by
giulia.cosenza
• 0
1
vote
2
replies
223
views
permutation test in edgeR
rna-seq
edgeR
updated 1 day ago by
Gordon Smyth
★ 7.0k • written 15 days ago by
Netanel
• 0
1
vote
3
replies
395
views
Limma compare between 3 conditions vs 2 conditions
Limma
updated 6 days ago by
Gordon Smyth
★ 7.0k • written 29 days ago by
Chris
▴ 260
0
votes
2
replies
336
views
How to add motifs in cellranger-arc reference?
gtf
scRNAseq
fasta
cellranger
updated 5 days ago by
Ehsan
• 0 • written 9 weeks ago by
bioinfo
▴ 150
1
vote
5
replies
578
views
Cell barcode whitelists for DNBelab C Series High-throughput Single-cell RNA Series Library Preparation Set?
cell-barcode
MGI
DNBelab
single-cell
updated 9 hours ago by
atowns21
• 0 • written 3 months ago by
benjamin.pyenson
• 0
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
3
replies
332
views
GTF file for Rhinolophus sinicus
Rhinolophus-sinicus
GTF
updated 1 hour ago by
GenoMax
141k • written 5 months ago by
ara
• 0
5
votes
3
replies
699
views
Illumina reads preprocessing best practice for snp calling applications
Illumina
snp
updated 4 days ago by
Enrique
• 0 • written 9 months ago by
Denis
▴ 310
2
votes
3
replies
936
views
Method to detect genome doubling
CNV
genome doubling
updated 1 day ago by
LauferVA
4.2k • written 4.5 years ago by
CY
▴ 750
0
votes
0
replies
272
views
Choice of relatedness cutoff for GWAS of a large cohort (>100K samples)
relatedness
IBD
GWAS
updated 1 day ago by
Ram
43k • written 14 months ago by
Oak
▴ 10
2
votes
4
replies
1.4k
views
How to fix Error in dat[, batch == batch_level] : (subscript) logical subscript too long when removing batch effects
microarray
combat
batch-effect
median-normalization
updated 5 days ago by
Ram
43k • written 18 months ago by
Dominique
• 0
1
vote
9
replies
1.2k
views
Supergnova stuck in tutorial
Genetic
Correlations
Python
Supergnova
Conda
updated 5 days ago by
Murat
• 0 • written 19 months ago by
Gerard
▴ 10
8
votes
6
replies
2.6k
views
bwa 0.7.18 download to fix compile fail with GCC 10
bwa
updated 6 days ago by
John Marshall
3.0k • written 23 months ago by
bioguy24
▴ 230
34
votes
16
replies
20k
views
9 follow
Filtration Of Reads With Length Lower Than 30 From Bam
read
length
bam
updated 4 days ago by
Hagen
▴ 10 • written 10.2 years ago by
filipzembol
▴ 180
1
vote
4
replies
1.4k
views
Removing/Accounting for batch effects in unbalanced group RNAseq data
rna-seq
batch-effect
deseq
updated 5 days ago by
Ram
43k • written 2.2 years ago by
claysandel
• 0
0
votes
4
replies
1.2k
views
Batch effects
Batch-effect
transcriptomics
updated 5 days ago by
Ram
43k • written 2.6 years ago by
BioQueen
▴ 30
326 results • Page
4 of 7
Recent Votes
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
Comment: TCGA2STAT Error: Firehose connection
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Comment: Redirection of Duplicate PMIDs
Answer: Redirection of Duplicate PMIDs
A: Should I Remove All Positions Containing A Gap In A Multiple Alignment Prior To
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Recent Replies
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
▴ 360
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.
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie
by
atowns21
• 0
Yes, that is a very good idea. Thanks for the help!
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie
by
GenoMax
141k
Only thing would be to try them out. See if you can detect them in the data you have. You could also simply look for unique representativ…
Comment: How to calculate identity percentage between proteins contained in a FASTA file?
by
GenoMax
141k
`clustal omega` can calculate distance matrix between two proteins (makes sense if your proteins are of similar size). You could try that: …
Comment: Should I use unpaired reads from trimmomatic
by
swbarnes2
14k
If the unpaired are _2, files, the _1 must exist somewhere. But the simple answer is probably going to be to just use all the _2 only. Yo…
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by
GenoMax
141k
> The needless granularity (fake precision) was obvious from the start You are assuming that all data generated is always of great quality…
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