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231 results • Page
1 of 5
Sort: Votes
Rank
Views
Votes
Replies
362
votes
82
replies
143k
views
35 follow
Tool:
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel
next-gen
ngs
updated 3 days ago by
jena
▴ 290 • written 11.1 years ago by
ole.tange
★ 4.4k
164
votes
70
replies
60k
views
34 follow
How To Efficiently Parse A Huge Fastq File?
fastq
next-gen-sequencing
updated 22 hours ago by
Ram
43k • written 12.7 years ago by
Panos
★ 1.8k
49
votes
30
replies
11k
views
13 follow
Tutorial:
How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation
meta
how-to
updated 1 day ago by
Istvan Albert
100k • written 8.1 years ago by
Ram
43k
31
votes
14
replies
12k
views
11 follow
Finding Rrna Genes In Metagenomic Data
rna
rRNA
metagenomics
updated 3 days ago by
Ram
43k • written 13.5 years ago by
toshnam
▴ 650
21
votes
6
replies
16k
views
survfit(Surv()) P-value interpretation for 3 survival curves?
survfit
Surv
survival curves
R
updated 5 days ago by
marshelma
• 0 • written 4.5 years ago by
JJDollar
▴ 130
16
votes
10
replies
663
views
6 follow
Forum:
F*up Night style events for Bioinformatics ? Comment if you're interested!
mistakes
updated 1 hour ago by
Madelaine Gogol
5.3k • written 22 hours ago by
Ann
★ 2.4k
16
votes
7
replies
12k
views
8 follow
MAF vs VAF
sequencing
updated 4 days ago by
Ömer An
▴ 260 • written 6.0 years ago by
lauren.wahyudi
▴ 50
15
votes
10
replies
7.5k
views
6 follow
Intersect multiple BED files
bed
intersect
updated 1 day ago by
Alex Reynolds
35k • written 8.2 years ago by
int11ap1
▴ 470
12
votes
7
replies
6.7k
views
Forum:
Differences between SMART-seq2, SMART-seq3, and 10x
cell
smartseq
UMIs
single
10x
updated 4 days ago by
dsull
★ 5.7k • written 2.6 years ago by
hamarillo
▴ 70
12
votes
14
replies
2.4k
views
8 follow
Forum:
Recovering bam files after unknown deletion in the storage
photorec
bam
sequencing
written 4.8 years ago by
Gabriel Wajnberg
▴ 70
11
votes
7
replies
894
views
Shrink logFC values after edgeR
logFC
edgeR
updated 5 days ago by
Gordon Smyth
★ 6.9k • written 8 weeks ago by
arvind.1
▴ 10
10
votes
6
replies
4.0k
views
Tutorial:
CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation
corlevelplot
updated 2 days ago by
Ram
43k • written 6.1 years ago by
Kevin Blighe
87k
9
votes
8
replies
5.6k
views
7 follow
CONTRA for CNV detection. troubleshooting
genome
next-gen-sequencing
cnv
software-error
updated 22 hours ago by
Ram
43k • written 9.8 years ago by
Kizuna
▴ 870
8
votes
6
replies
409
views
Pangenome of plant
pangenome
plant
updated 1 day ago by
talbots
• 0 • written 2 days ago by
analyst
▴ 10
7
votes
2
replies
203
views
Create a new reference genome with denovo assembly and standard reference with long read data?
PacBio
updated 2 days ago by
gconcepcion
▴ 410 • written 2 days ago by
eorr
▴ 30
6
votes
9
replies
1.8k
views
How to convert .wib files to .wig or .bed?
wib
BED
wig
bedtools
2 days ago by
Zeng Jingyu
▴ 60
6
votes
13
replies
487
views
Allocating right resources to HPC using LSF scheduler
BWA
GATK
hpc
lsf
bsub
3 days ago by
Maverick
▴ 10
6
votes
12
replies
5.5k
views
6 follow
Getting sample information from GEO
GEO
NCBI
updated 2 days ago by
Tania
• 0 • written 6.9 years ago by
Tom_L
▴ 350
6
votes
7
replies
623
views
cutadapt not trimming all adapters in PE Illumina sequencing
NGS
Illumina
cutadapt
6 days ago by
joe
▴ 470
5
votes
8
replies
2.2k
views
VariantCalling with single sanger read
snps
blast
indel
Variant-Calling
updated 3 days ago by
Ram
43k • written 7.6 years ago by
Amirosein
▴ 70
5
votes
15
replies
4.8k
views
6 follow
Why are there many reads with green color in IGV of RNA-seq data?
rna-seq
IGV
mapping
updated 6 days ago by
vague-barracuda-4686
• 0 • written 4.7 years ago by
Apprentice
▴ 160
5
votes
5
replies
5.4k
views
beagle 4 exception: Duplicate marker
vcf
IBD
plink
beagle
updated 2 days ago by
Ram
43k • written 9.3 years ago by
galbarel
▴ 10
5
votes
2
replies
325
views
Forum:
Can questions and answers on biostars be asked only in English? Can't I use Russian for example?
language
updated 4 days ago by
Michael
54k • written 4 days ago by
avpuzanov
• 0
4
votes
3
replies
1.2k
views
GATK best practices for Broad-produced NGS data
NGS
GATK4
BroadInstitute
Variant-Calling
updated 3 days ago by
Ram
43k • written 5.3 years ago by
Mehulsharma.253
▴ 30
4
votes
12
replies
3.4k
views
How to read VCF (v4.1) file? (student project) (samtools version 0.1.19)
variant-calling
samtools
VCF
BCF
updated 3 days ago by
Ram
43k • written 5.5 years ago by
c.clarido
▴ 110
4
votes
9
replies
942
views
Error in openning FastQC
fastqc
igv
updated 16 hours ago by
GenoMax
140k • written 7 months ago by
huynhthienphai
• 0
4
votes
11
replies
1.2k
views
Paired layout, but one fastq file
fastq
updated 1 day ago by
GenoMax
140k • written 12 months ago by
Andy
▴ 120
4
votes
2
replies
3.3k
views
Genome annotation: convert gtf to gff3 file
gff3
gtf
updated 3 days ago by
vague-barracuda-4686
• 0 • written 16 months ago by
shinyjj
▴ 50
4
votes
9
replies
671
views
Snakemake >= version 8 cluster configuration and SLURM job submission
parallelization
slurm
snakemake
cluster
updated 3 days ago by
Simon
▴ 10 • written 7 days ago by
Maxwell
▴ 20
4
votes
14
replies
4.5k
views
8 follow
Installation: Tax4Fun2 package are not found and github repository is not maintained anymore
Tax4Fun2
updated 1 day ago by
Ram
43k • written 21 months ago by
Elsa
▴ 20
3
votes
10
replies
657
views
Intersect gene IDs list and GFF3 to get the annotation.
annotation
GFF
6 days ago by
Lissa Cruz Saavedra
• 0
3
votes
12
replies
644
views
Facing problem with extracting phenotypic data from GEO
WGCNA
GEO
2 days ago by
bioinfo_enthusiast
• 0
3
votes
0
replies
128
views
Herald:
The Biostar Herald for Monday, March 25, 2024
herald
4 days ago by
Biostar
2.6k
3
votes
5
replies
593
views
How to filter Illumina Nirvana variant annotation?
nirvana
filtration
updated 5 days ago by
Pierre Lindenbaum
160k • written 5 days ago by
Kauno tvirtovės
• 0
3
votes
13
replies
445
views
Variant calling of GBS data
GBS
variants
BQSR
21 hours ago by
analyst
▴ 10
3
votes
7
replies
525
views
Blast NCBI online using R
R
NCBI
BLAST
Rstudio
2 days ago by
Begonia_pavonina
▴ 140
3
votes
5
replies
588
views
somatic variant calling without matched normal in long-reads
variants
cancer
illumina
ONT
nanopore
3 days ago by
eesiribloom
▴ 50
3
votes
5
replies
381
views
Losing my mind with a VCF problem
vcf
bcftools
updated 6 days ago by
Michael
54k • written 6 days ago by
a.beggs
▴ 30
3
votes
2
replies
294
views
FDR and Bonferroni
FDR
Bonferroni
updated 1 day ago by
joe
▴ 470 • written 3 days ago by
song
• 0
3
votes
2
replies
121
views
Gene reads all zero for each sample
R
salmon
DE
DESeq2
22 hours ago by
DYLAN NICO
• 0
2
votes
1
reply
301
views
Tool:
TGSFilter, An ultra-fast and efficient tool for long reads filtering and trimming
genome-assembly
filtering
reads
trimming
updated 4 days ago by
Yingzi
• 0 • written 5 days ago by
Huiyang
▴ 180
2
votes
1
reply
2.5k
views
CRAM reference registry and the GRch38 reference genome
BAM
Samtools
GRCh38
CRAM
Variant-Calling
updated 3 days ago by
Ram
43k • written 5.3 years ago by
Mehulsharma.253
▴ 30
2
votes
5
replies
453
views
Searching for gene in multiple genomes
gene
genome
alignment
sequence
updated 6 days ago by
BioinfGuru
★ 1.6k • written 7 days ago by
Miya
• 0
2
votes
2
replies
230
views
singlecell annotation
scRNA-seq
annotation
2 days ago by
kayah
• 0
2
votes
5
replies
1.8k
views
alignement and Variant calling with BWA and samtools
variant-calling
samtools
BWA
updated 3 days ago by
Ram
43k • written 2.9 years ago by
simon.burgermeister
▴ 30
2
votes
3
replies
479
views
Should I use Dfam or a custom repetitve elements library (from PlantRep) as a repeat database; using RepeatMasker in a Linux machine?
genome
sequence
repeatmasker
blast
updated 2 days ago by
b.contreras.moreira
▴ 70 • written 3 days ago by
Vijith
▴ 30
2
votes
2
replies
217
views
A pipeline for prediction and annotation of obelisks
rna-seq
updated 1 day ago by
Pierre Lindenbaum
160k • written 2 days ago by
fred.s.kremer
▴ 110
2
votes
7
replies
599
views
Selecting query format for repeated calls to NCBI's API
NCBI
esummary
elink
API
efetch
updated 3 days ago by
GenoMax
140k • written 5 weeks ago by
LauferVA
4.1k
2
votes
4
replies
354
views
Visualizing human genomic loci
Genome
visualization
3 days ago by
James
▴ 10
2
votes
1
reply
301
views
GIS overlay for environmental samples from NCBI
NCBI
environmental
SRA
GIS
ArcPro
6 days ago by
joe
▴ 470
231 results • Page
1 of 5
Recent Votes
Answer: Is RNAseq data from a monoclonal cell line technically considered scRNAseq?
F*up Night style events for Bioinformatics ? Comment if you're interested!
Announcement: Research Topic "Mechanistic, Machine Learning and Hybrid Models of the 'Other' Endocrine Regulatory Systems in Health and Disease", Volume II
Comment: Number of CPUs to use by DRAP for transcriptomic assmbly
Comment: Gene reads all zero for each sample
Synthetic lethality and cancer database
Answer: log2(TPM+1)
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Recent Replies
Comment: Error running local blastn in R using system2
by
Harrison
• 0
Yes, in my actual script I use the whole path to nt_euk. I was just showing `C:/data/nt_euk` as shorthand for the full path. There are no s…
Comment: Error running local blastn in R using system2
by
Harrison
• 0
I am seeing `'cat' is not recognized as an internal or external command, operable program or batch file.`
Comment: Alignment with new reference
by
GenoMax
140k
> I'd like to realign my sequences to a reference that doesn't include > the base segment corresponding to the enzyme interval. How can I >…
Comment: How do I get the gene annotations as a text file from a genebank file?
by
GenoMax
140k
You will have to use a programming approach. BioPython is one option: https://warwick.ac.uk/fac/sci/moac/people/students/peter_cock/python/…
Comment: Number of CPUs to use by DRAP for transcriptomic assmbly
by
GenoMax
140k
> Is it because implementing multi-threading requires additional effort on their part Yes but in addition considerations here are importan…
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Madelaine Gogol
5.3k
That sounds fun, and I've got some of these that I have told many people about (to keep them from making the same mistakes as me). I am pla…
Comment: Mapping ortholog human and mouse transcript
by
1769mkc
★ 1.2k
for hgnc and ensembl that can be done for transcript id for human to mouse ortholog its difficult to parse and map the exact version from g…
Comment: Announcement: Research Topic "Mechanistic, Machine Learning and Hybrid Models of
by
Mensur Dlakic
★ 26k
Take it from someone who has hosted both a successful and a failed research topic: these deadlines are unrealistic. I am guessing you are p…
Answer: Tissue specific mRNA expression dataset in human and mouse
by
BioinfGuru
★ 1.6k
Awesome, years ago I wrote my thesis on the use of Tau to calculate tissue specificity, enjoy! The supplementary materials in the paper is…
Answer: Mapping ortholog human and mouse transcript
by
BioinfGuru
★ 1.6k
That error is on the server side, nothing to do with you, and is very common. Usually the fix is to try again in an hour, or to insert host…
Comment: Nanopore multisample variant calling
by
emilydolivo97
• 0
hello @colindaven , Did you find a suitable tool for this purpose please ? I'm dealing with fungal dataset
Comment: How do I get the gene annotations as a text file from a genebank file?
by
BioinfGuru
★ 1.6k
Can you upload or post a link to the genbank file please?
Comment: Mapping ortholog human and mouse transcript
by
manaswwm
▴ 490
I usually perform biomaRt queries with their `getBM()` function where I list the input using `filter` and `values` option and my request in…
Comment: DESeq2 and normalization
by
JH
• 0
Thank you for your response. I have often seen commands like dds <- estimateSizeFactors(dds) normalized_counts <- counts(dds, normalized=T…
Comment: Number of CPUs to use by DRAP for transcriptomic assmbly
by
Mohamed Abderrahmane
▴ 10
It's the case that there's no indication of multi-threading in the documentation. However, it made me wonder why the developers would restr…
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