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683 results • Page
4 of 14
Sort: replies
Rank
Views
Votes
Replies
0
votes
5
replies
335
views
A question about reference genome for creating the consensus sequence
fasta
fa
cram
genome
10 days ago by
me
• 0
0
votes
4
replies
407
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
5 days ago by
beginner123
• 0
1
vote
4
replies
349
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 4 days ago by
Juke34
8.6k • written 5 days ago by
Vijith
▴ 30
6
votes
4
replies
13k
views
Trimmomatic: What is the difference between paired and unpaired output files in paired-end mode
trimmomatic
paired-end
updated 7 days ago by
Ruqaiya
• 0 • written 6.5 years ago by
dllopezr
▴ 130
0
votes
4
replies
309
views
Genbank File Format
gbkformat
18 days ago by
alenew.am
• 0
1
vote
4
replies
288
views
Filtering VCF files based on VAF giving incorrect results
bcftools
GATK
Bioinformatics
picard
VCF
3 days ago by
Arton
▴ 10
1
vote
4
replies
451
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
19 days ago by
hagl
▴ 10
3
votes
4
replies
326
views
Truncated metadata file report from ENA Portal API
ena
python
8 days ago by
Giulia
• 0
0
votes
4
replies
666
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
29 days ago by
Kai Xin
• 0
1
vote
4
replies
397
views
Understanding STAR output (Aligned.out.sam file)
STAR
paired-end
read
11 days ago by
heelpPlease
• 0
0
votes
4
replies
624
views
how to find genes that are significantly expressed in brain cortex samples
rna-seq
gene-expression
updated 28 days ago by
ATpoint
82k • written 29 days ago by
rheab1230
▴ 140
2
votes
4
replies
341
views
from row count to tpm
tpm
row-count
normalization
updated 18 days ago by
Ram
43k • written 26 days ago by
michelafrancesconi9
▴ 20
3
votes
4
replies
4.0k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 10 days ago by
chloek88
• 0 • written 5.6 years ago by
Philipp Bayer
8.5k
2
votes
4
replies
5.6k
views
44% Successfully Assigned Fragments with featureCounts after 85% uniquely mapped reads with STAR
rna-seq
alignment
RNA-Seq
featureCounts
STAR
updated 5 days ago by
Thind amarinder
▴ 340 • written 5.0 years ago by
garbuzov
▴ 70
2
votes
4
replies
720
views
Count all variants from vcf file
variants
vcf
Count
updated 11 days ago by
Pierre Lindenbaum
161k • written 21 months ago by
t.ali
• 0
0
votes
4
replies
241
views
Sequencing Depth (Read Depth) Calculations
depth
3 days ago by
LucisTheFather
• 0
0
votes
4
replies
423
views
Highest variable features in single cell data
single-cell
11 days ago by
carolofharvest
▴ 40
3
votes
4
replies
478
views
Design matrix Differential expression analysis
RNA-seq
Differential-expression
updated 12 days ago by
Gordon Smyth
★ 7.2k • written 15 days ago by
SHN
▴ 40
3
votes
4
replies
754
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
26 days ago by
rahu
• 0
0
votes
4
replies
300
views
How to extract cells of different species after mapping with combined genome?
snRNA-seq
scRNA-seq
updated 1 day ago by
Tony
• 0 • written 3 days ago by
vk
▴ 10
0
votes
4
replies
2.7k
views
Lositan freezing when generating selection table
LOSITAN
updated 24 days ago by
evawillms183
• 0 • written 8.3 years ago by
andrepleao
• 0
0
votes
4
replies
342
views
Perfom a Gene Ontology Analysis from GO terms txt file
RNA-Seq
GO
updated 18 days ago by
Ram
43k • written 19 days ago by
Hamtaro
▴ 50
1
vote
4
replies
492
views
GTF file for Rhinolophus sinicus
Rhinolophus-sinicus
GTF
updated 24 days ago by
atowns21
• 0 • written 6 months ago by
ara
• 0
0
votes
4
replies
262
views
Galaxy StringTie error
stringtie
galaxy
4 days ago by
trkfs
• 0
1
vote
4
replies
291
views
Add stats to boxplot in R
stats
R
3 days ago by
Ghada
• 0
0
votes
4
replies
289
views
How to handle duplicated genes in TCGA data?
TCGA
GDC
mRNA
updated 17 hours ago by
txema.heredia
▴ 130 • written 2 days ago by
Ngrin
• 0
2
votes
4
replies
385
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
24 days ago by
samuelkalandarov2002
▴ 10
0
votes
4
replies
3.6k
views
SNPEff database building error
SNP
updated 5 days ago by
Fungal genetics
• 0 • written 7.1 years ago by
ntyagi654
• 0
3
votes
4
replies
424
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
23 days ago by
QX
• 0
6
votes
4
replies
312
views
Details on salmon index
Salmon
updated 1 day ago by
Rob
6.6k • written 2 days ago by
Lorenzo
• 0
5
votes
4
replies
725
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
24 days ago by
kirillkirilenko
▴ 40
2
votes
4
replies
2.5k
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 23 days ago by
ZhangYuanfeng
• 0 • written 2.5 years ago by
Frazier Baker
• 0
2
votes
4
replies
400
views
Should I use unpaired reads from trimmomatic
RNA-seq
QC
Trimmomatic
updated 25 days ago by
swbarnes2
14k • written 26 days ago by
dxj294
• 0
2
votes
4
replies
272
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell
seurat
10XGenomics
scRNAseq
updated 3 days ago by
yura.grabovska
▴ 90 • written 3 days ago by
ev97
▴ 20
2
votes
4
replies
416
views
What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
ChIP-seq
25 days ago by
HyperEvo
• 0
1
vote
4
replies
409
views
Segmentation error while using a tool
smalt
updated 14 days ago by
Mensur Dlakic
★ 27k • written 14 days ago by
Ruqaiya
• 0
0
votes
4
replies
310
views
Correlation Analysis
statistics
methylation
NGS
expression
7 days ago by
Researcher
▴ 30
2
votes
4
replies
303
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
3 days ago by
Esraa
• 0
2
votes
4
replies
231
views
Help with IGV abbreviation
igv
updated 4 days ago by
Ram
43k • written 5 days ago by
GeneC
• 0
1
vote
4
replies
1.1k
views
Filtering qscore on dorado
dorado
filtering
QC
nanopore
Guppy
16 days ago by
eebloom
▴ 80
3
votes
4
replies
386
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR
masspec
uORF
peptide
updated 2 days ago by
GenoMax
142k • written 2 days ago by
Pierre Lindenbaum
161k
1
vote
4
replies
420
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 8 days ago by
GenoMax
142k • written 4 weeks ago by
aniigodwinn
• 0
1
vote
4
replies
344
views
Contig assembly task, errors
dna
genetics
contig
assembly
updated 5 days ago by
Ram
43k • written 10 days ago by
samRayne
• 0
1
vote
4
replies
502
views
cellranger error message
multiplexing
cellranger
updated 8 days ago by
Max
• 0 • written 3 months ago by
Alivia
▴ 10
6
votes
4
replies
445
views
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
16 days ago by
Estevão
▴ 10
2
votes
4
replies
278
views
Where to get the following bed file?
WES
bed
reference
file
updated 12 days ago by
GenoMax
142k • written 12 days ago by
wyuan37
• 0
1
vote
4
replies
311
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 15 hours ago by
Joe
21k • written 10 days ago by
cput
• 0
0
votes
4
replies
275
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
18 hours ago by
mavy
▴ 10
2
votes
4
replies
2.7k
views
When to use .vcf or .gvcf files from GATK HaplotypeCaller?
indel
gatk
calling
snp
variant
updated 19 days ago by
Medhat
9.7k • written 2.0 years ago by
Vitor1
▴ 120
3
votes
4
replies
301
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq
patch
freeze
genome
updated 1 day ago by
Jeremy Leipzig
22k • written 2 days ago by
Ali
• 0
683 results • Page
4 of 14
Recent Votes
A: How is the design in DESeq2 work?
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
Answer: RNAseq coverage vs depth for transcript isoform expression?
constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Answer: RNAseq coverage vs depth for transcript isoform expression?
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Popular Question
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synat.keam
▴ 100
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jv
★ 1.8k
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syedahamdani94
• 0
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Recent Replies
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors)
by
nguyenn6
• 0
did you ever figure it out? i'm having the same issue.
Comment: Traveler with Infernal mapping failed
by
anton.i.petrov
• 0
Hi Larissa! I am the lead developer of R2DT and I've just noticed this question. Could you please email help@r2dt.bio with your input seque…
Comment: constructing pangenome through psvcp
by
analyst
▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
Comment: calculating genomic coverage/ base overlap in R
by
1769mkc
★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks
by
ATpoint
82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner
by
Joe
21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression?
by
Gordon Smyth
★ 7.2k
See the exploration of isoform estimation precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167.…
Comment: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA
by
mavy
▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object
by
Alex Reynolds
35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF)
by
aidangcruickshank
▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data?
by
Ngrin
• 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2
by
swbarnes2
14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
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