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681 results • Page
1 of 14
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Views
Votes
Replies
76
votes
72
replies
20k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
24 days ago by
Kevin Blighe
88k
40
votes
10
replies
43k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma
sva
Combat
batch-effect
updated 19 days ago by
cwwong13
▴ 40 • written 6.8 years ago by
lessismore
★ 1.3k
38
votes
24
replies
2.3k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 18 days ago by
i.sudbery
19k • written 21 days ago by
noodle
▴ 580
38
votes
12
replies
31k
views
9 follow
How to systematically check if a bam file is truncated
Exomeseq
updated 1 day ago by
alanh
▴ 170 • written 7.1 years ago by
jonessara770
▴ 240
29
votes
28
replies
34k
views
11 follow
Split Fastq Files Into Chunks Of 1M Reads
split
fastq
updated 16 days ago by
thomas.heigl.ibk
• 0 • written 12.8 years ago by
Bioscientist
★ 1.7k
25
votes
11
replies
3.8k
views
6 follow
Forum:
Site Use Guidelines
meta
biostars
Guidelines
updated 25 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 22 days ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
16
votes
12
replies
7.5k
views
10 follow
how to split multi-fasta file into single fasta file named by header
genome
perl
python3
bash
python
updated 16 days ago by
rsieber
▴ 10 • written 3.2 years ago by
Kumar
▴ 120
14
votes
2
replies
7.1k
views
Trouble with Pilon installation
polishing
pilon
installation
updated 24 days ago by
Lissa Cruz Saavedra
• 0 • written 7.3 years ago by
Rox
★ 1.4k
13
votes
14
replies
960
views
High Malat-1 expression in single cell data
single-cell
updated 11 days ago by
t.montserrat.ayuso
▴ 40 • written 19 days ago by
carolofharvest
▴ 40
11
votes
3
replies
347
views
TFs and Gene databases
Transcription-factor
Target
Regulatory-Networks
updated 10 days ago by
b.contreras.moreira
▴ 200 • written 11 days ago by
ijarne
• 0
10
votes
6
replies
10k
views
6 follow
CDS vs cDNA vs transcript for mapping RNA-Seq reads
Assembly
rna-seq
alignment
updated 22 days ago by
Antonio R. Franco
★ 5.1k • written 6.0 years ago by
williamsbrian5064
▴ 520
10
votes
16
replies
17k
views
7 follow
How Can I Count Snps In My Final Vcf Files
SNP
updated 12 days ago by
Pierre Lindenbaum
161k • written 5.8 years ago by
mostafarafiepour
▴ 180
10
votes
14
replies
798
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 11 days ago by
GenoMax
142k • written 17 days ago by
nicole.kavanagh
• 0
9
votes
23
replies
9.8k
views
Tool:
BioLabDonkey - new Mac program for molecular biologists
software
biolabdonkey
7 days ago by
vytarasov
▴ 180
9
votes
7
replies
7.2k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 7 days ago by
Ruqaiya
• 0 • written 5.7 years ago by
xiaozhongzhiping
▴ 20
9
votes
13
replies
4.8k
views
Custom Reference panel creation for data imputation from .vcf files
imputation
reference panel
updated 8 days ago by
analyst
▴ 50 • written 6.4 years ago by
David_emir
▴ 490
8
votes
16
replies
1.2k
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 22 days ago by
bk11
★ 2.5k • written 10 weeks ago by
Sofia
• 0
8
votes
8
replies
767
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 24 days ago by
swbarnes2
14k • written 25 days ago by
Aaliya
▴ 10
8
votes
5
replies
6.6k
views
ISCN annotation for SV/CN VCF files
SV
written 8 months ago by
a.beggs
▴ 60
7
votes
7
replies
6.0k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq
SNP
updated 23 days ago by
rohitsatyam102
▴ 870 • written 6.2 years ago by
smallfish
▴ 10
7
votes
6
replies
604
views
Filtering sam or bam file with maximum matching region
crisper-edited
alignment
match
27 days ago by
analyst
▴ 50
7
votes
2
replies
330
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 25 days ago by
geneontologyhelp
▴ 400 • written 26 days ago by
catherine.teyssier
• 0
7
votes
16
replies
959
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
20 days ago by
Ruqaiya
• 0
7
votes
1
reply
197
views
Tutorial:
removeBatchEffect explained using base R linear models
limma
effects
batch
removebatcheffects
updated 11 days ago by
dariober
14k • written 11 days ago by
nhaus
▴ 360
6
votes
6
replies
1.8k
views
agilent human all exon sureselct v7 bed file
exon
human
bed
v7
agilent
all
sureselect
updated 13 days ago by
MiladAD
▴ 10 • written 2.0 years ago by
soheil
• 0
6
votes
4
replies
445
views
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
16 days ago by
Estevão
▴ 10
6
votes
5
replies
2.3k
views
Tophat multiple or unique mapping criteria
RNA-Seq
updated 6 days ago by
Ruqaiya
• 0 • written 6.7 years ago by
maple964
• 0
6
votes
7
replies
394
views
Longest transcript variant per gene
transcript
longest
variant
orthofinder
6 days ago by
sansan_96
▴ 90
6
votes
5
replies
1.7k
views
How to calculate coverage of Nanopore long read data?
sequencing
coverage
4 days ago by
Arton
▴ 10
6
votes
2
replies
244
views
EdgeR - relationship between logFC and coefficients
differential-expression
r
edger
updated 9 days ago by
Gordon Smyth
★ 7.2k • written 9 days ago by
gBioStar5
▴ 10
6
votes
4
replies
322
views
Details on salmon index
Salmon
updated 1 day ago by
Rob
6.6k • written 2 days ago by
Lorenzo
• 0
6
votes
3
replies
234
views
Interpretting IGV output
IGV
updated 27 days ago by
Carlo Yague
8.7k • written 27 days ago by
analyst
▴ 50
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
5
votes
2
replies
350
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 20 days ago by
i.sudbery
19k • written 22 days ago by
vanbelj
▴ 40
5
votes
7
replies
501
views
RNA seq analysis
DESeq
RNA-seq
4 days ago by
Jacek
▴ 20
5
votes
3
replies
321
views
6 follow
Integrate transcriptomic data and proteomics data.
OMICS
updated 19 days ago by
Lluís R.
★ 1.2k • written 19 days ago by
이민경[학생](대학원 융합의과학과)
• 0
5
votes
2
replies
443
views
Missing protein (VEGF-A) in String db
VGFA
stringdb
updated 23 days ago by
shalespringer
▴ 10 • written 3 months ago by
Phenylananin
▴ 20
5
votes
4
replies
725
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
25 days ago by
kirillkirilenko
▴ 40
5
votes
13
replies
2.0k
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
updated 28 days ago by
ATpoint
82k • written 29 days ago by
BioinfGuru
★ 1.7k
5
votes
3
replies
760
views
Illumina reads preprocessing best practice for snp calling applications
Illumina
snp
updated 29 days ago by
Enrique
• 0 • written 10 months ago by
Denis
▴ 310
5
votes
5
replies
325
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
11 days ago by
Chris
▴ 280
5
votes
5
replies
355
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA
DADA2
metabarcoding
updated 16 days ago by
atharvakarkare14
▴ 40 • written 16 days ago by
Begonia_pavonina
▴ 150
5
votes
6
replies
607
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 18 days ago by
me
▴ 760 • written 19 days ago by
Mariana
▴ 40
5
votes
5
replies
673
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 15 days ago by
Mbofire
• 0 • written 24 days ago by
Ming Tommy Tang
★ 3.9k
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq
RNA-Seq
exon
updated 12 days ago by
Sara
▴ 30 • written 6.7 years ago by
Lila M
★ 1.2k
4
votes
6
replies
3.9k
views
Taking the difference of two VCFs (or removing singletons)
genome
sequencing
singleton
SNP
filter
updated 18 days ago by
Andres
▴ 20 • written 9.7 years ago by
hermathena
▴ 40
4
votes
1
reply
207
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
4 days ago by
J.
▴ 40
4
votes
9
replies
2.2k
views
6 follow
Same sequencing sample in multiple lanes. How to analyse it?
sequencing
bowtie2
alignment
samtools
ngs
updated 15 days ago by
ST
• 0 • written 2.2 years ago by
Federico
• 0
4
votes
7
replies
616
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 24 days ago by
dsull
★ 6.0k • written 25 days ago by
VITALA
• 0
681 results • Page
1 of 14
Recent Votes
Interpreting the Jackstraw plot of Seurat
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Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
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Answer: CellRanger output more cells than specified using --force-cells? Why?
by
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▴ 30
I actually had this same issue with CellRanger v7- turns out that since you have 2 species in your mapping reference, CellRanger is forcing…
Answer: Checking chromosome builds for genotyping data
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Muhammad
• 0
Assume you have genotype data in Plink format. (G.bed, G.bim, G.fam) Download some reference panel data in Plink format (R.bed, R.bim, R.f…
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors)
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nguyenn6
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did you ever figure it out? i'm having the same issue.
Comment: Traveler with Infernal mapping failed
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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
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Fixed the issue by updating nucmer version.
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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
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★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
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82k
What is your question? It's unclear.
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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.…
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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…
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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
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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 -…
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Yes, `bedmap` will perform operations on one or two BED files.
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Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
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