Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : this week
all time
today
this week
this month
this year
228 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 1 day ago by
jena
▴ 290 • written 11.1 years ago by
ole.tange
★ 4.4k
49
votes
29
replies
11k
views
13 follow
Tutorial:
How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation
meta
how-to
updated 1 hour ago by
ATpoint
81k • 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 2 days ago by
Ram
43k • written 13.5 years ago by
toshnam
▴ 650
26
votes
5
replies
23k
views
BLAST options: max_target_seqs and num_alignments
blast
updated 6 days ago by
Lada
▴ 30 • written 9.4 years ago by
biolab
★ 1.4k
21
votes
6
replies
16k
views
survfit(Surv()) P-value interpretation for 3 survival curves?
survfit
Surv
survival curves
R
updated 4 days ago by
marshelma
• 0 • written 4.5 years ago by
JJDollar
▴ 130
16
votes
7
replies
12k
views
8 follow
MAF vs VAF
sequencing
updated 3 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 16 hours ago by
Alex Reynolds
35k • written 8.2 years ago by
int11ap1
▴ 470
15
votes
6
replies
594
views
Need consultation about my rna-seq workflow
RNA-seq
Gene-expression
updated 6 days ago by
Ram
43k • written 8 days ago by
markusz
▴ 10
12
votes
7
replies
6.7k
views
Forum:
Differences between SMART-seq2, SMART-seq3, and 10x
cell
smartseq
UMIs
single
10x
updated 3 days ago by
dsull
★ 5.6k • 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 4 days ago by
Gordon Smyth
★ 6.9k • written 7 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 1 day ago by
Ram
43k • written 6.1 years ago by
Kevin Blighe
87k
8
votes
6
replies
370
views
Pangenome of plant
pangenome
plant
updated 16 hours ago by
talbots
• 0 • written 1 day ago by
analyst
▴ 10
7
votes
2
replies
196
views
Create a new reference genome with denovo assembly and standard reference with long read data?
PacBio
updated 1 day ago by
gconcepcion
▴ 410 • written 1 day ago by
eorr
▴ 30
7
votes
7
replies
3.3k
views
How to perform normalization when converting ATAC bam file to bigwig file using deeptools for IGV visualization
bamCoverage
deeptools
bigwig
IGV
ATAC
updated 5 days ago by
sgv
• 0 • written 2.2 years ago by
sir.outman
▴ 40
6
votes
7
replies
621
views
cutadapt not trimming all adapters in PE Illumina sequencing
NGS
Illumina
cutadapt
5 days ago by
joe
▴ 470
6
votes
12
replies
5.5k
views
6 follow
Getting sample information from GEO
GEO
NCBI
updated 1 day ago by
Tania
• 0 • written 6.8 years ago by
Tom_L
▴ 350
6
votes
13
replies
467
views
Allocating right resources to HPC using LSF scheduler
BWA
GATK
hpc
lsf
bsub
2 days ago by
Maverick
▴ 10
6
votes
9
replies
1.7k
views
How to convert .wib files to .wig or .bed?
wib
BED
wig
bedtools
1 day ago by
Zeng Jingyu
▴ 60
5
votes
8
replies
2.2k
views
VariantCalling with single sanger read
snps
blast
indel
Variant-Calling
updated 1 day ago by
Ram
43k • written 7.6 years ago by
Amirosein
▴ 70
5
votes
15
replies
4.7k
views
6 follow
Why are there many reads with green color in IGV of RNA-seq data?
rna-seq
IGV
mapping
updated 5 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 1 day ago by
Ram
43k • written 9.3 years ago by
galbarel
▴ 10
5
votes
2
replies
321
views
Forum:
Can questions and answers on biostars be asked only in English? Can't I use Russian for example?
language
updated 3 days ago by
Michael
54k • written 3 days ago by
avpuzanov
• 0
4
votes
2
replies
3.3k
views
Genome annotation: convert gtf to gff3 file
gff3
gtf
updated 2 days ago by
vague-barracuda-4686
• 0 • written 16 months ago by
shinyjj
▴ 50
4
votes
9
replies
663
views
Snakemake >= version 8 cluster configuration and SLURM job submission
parallelization
slurm
snakemake
cluster
updated 2 days ago by
Simon
▴ 10 • written 6 days ago by
Maxwell
▴ 20
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 1 day ago by
Ram
43k • written 5.5 years ago by
c.clarido
▴ 110
4
votes
11
replies
1.2k
views
Paired layout, but one fastq file
fastq
updated 7 hours ago by
GenoMax
140k • written 12 months ago by
Andy
▴ 120
4
votes
3
replies
1.2k
views
GATK best practices for Broad-produced NGS data
NGS
GATK4
BroadInstitute
Variant-Calling
updated 1 day ago by
Ram
43k • written 5.3 years ago by
Mehulsharma.253
▴ 30
4
votes
14
replies
4.5k
views
8 follow
Installation: Tax4Fun2 package are not found and github repository is not maintained anymore
Tax4Fun2
updated 16 hours ago by
Ram
43k • written 21 months ago by
Elsa
▴ 20
4
votes
3
replies
403
views
Single cluster spanning in different locations in UMAP in scRNAseq data
UMAP
scRNAseq
6 days ago by
sarahmanderni
▴ 100
3
votes
7
replies
522
views
Blast NCBI online using R
R
NCBI
BLAST
Rstudio
1 day ago by
Begonia_pavonina
▴ 140
3
votes
5
replies
583
views
somatic variant calling without matched normal in long-reads
variants
cancer
illumina
ONT
nanopore
2 days ago by
eesiribloom
▴ 50
3
votes
0
replies
120
views
Herald:
The Biostar Herald for Monday, March 25, 2024
herald
2 days ago by
Biostar
2.6k
3
votes
2
replies
255
views
FDR and Bonferroni
FDR
Bonferroni
updated 8 hours ago by
joe
▴ 470 • written 2 days ago by
song
• 0
3
votes
5
replies
583
views
How to filter Illumina Nirvana variant annotation?
nirvana
filtration
updated 3 days ago by
Pierre Lindenbaum
160k • written 3 days ago by
Kauno tvirtovės
• 0
3
votes
10
replies
651
views
Intersect gene IDs list and GFF3 to get the annotation.
annotation
GFF
5 days ago by
Lissa Cruz Saavedra
• 0
3
votes
5
replies
376
views
Losing my mind with a VCF problem
vcf
bcftools
updated 5 days ago by
Michael
54k • written 5 days ago by
a.beggs
▴ 30
3
votes
12
replies
621
views
Facing problem with extracting phenotypic data from GEO
WGCNA
GEO
1 day ago by
bioinfo_enthusiast
• 0
3
votes
5
replies
749
views
Error in openning FastQC
fastqc
igv
updated 22 hours ago by
GenoMax
140k • written 7 months ago by
huynhthienphai
• 0
2
votes
6
replies
3.3k
views
Base Quality of a reported variant in VCF
alignment
FASTQ
VCF
next-gen
Variant-Calling
updated 1 day ago by
Ram
43k • written 9.1 years ago by
VineethVenumadhavan
▴ 50
2
votes
2
replies
220
views
Infering the cell composition from bulk RNA-seq data for mouse
RNA-seq
deconvolution
mouse
5 days ago by
feather-W
• 0
2
votes
4
replies
3.6k
views
Tutorial for analysing gpr files of microarray
GPR
microarray
updated 6 days ago by
bioyas
▴ 10 • written 5.4 years ago by
afli
▴ 190
2
votes
5
replies
974
views
Why multiple SYMBOLS, Consequences... for Variant Effect Predictor (VEP)
VEP
updated 1 day ago by
barslmn
★ 2.1k • written 15 months ago by
gernophil
▴ 80
2
votes
2
replies
199
views
Location of NCBI ftp site changed?
ftp
ncbi
1 day ago by
sampsa.hyvamaki
• 0
2
votes
6
replies
452
views
Need help understanding core SNPs
SNPs
snippy
3 days ago by
ujichu
• 0
2
votes
4
replies
1.6k
views
bowtie2 maximum value of MAPQ
bowtie2
bowtie
updated 2 days ago by
axol0tl
• 0 • written 3.6 years ago by
sami
▴ 30
2
votes
2
replies
4.3k
views
Variant calling for sanger reads
variant-calling
sanger
alignment
variants
updated 1 day ago by
Ram
43k • written 7.6 years ago by
Amirosein
▴ 70
2
votes
3
replies
213
views
Reference mouse phased vcf
mm10
vcf
phasing
Beagle
3 days ago by
machoo
• 0
2
votes
1
reply
2.5k
views
CRAM reference registry and the GRch38 reference genome
BAM
Samtools
GRCh38
CRAM
Variant-Calling
updated 1 day ago by
Ram
43k • written 5.3 years ago by
Mehulsharma.253
▴ 30
2
votes
1
reply
300
views
Tool:
TGSFilter, An ultra-fast and efficient tool for long reads filtering and trimming
genome-assembly
filtering
reads
trimming
updated 3 days ago by
Yingzi
• 0 • written 4 days ago by
Huiyang
▴ 180
228 results • Page
1 of 5
Recent Votes
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
Answer: Hybrid assembly Pacbio- Nanopore
C: Why is 0/0 homozygous reference call in VCF useful information?
Answer: snippy error
Answer: TSS of protein coding genes
TSS of protein coding genes
Answer: vcf not indexing
Recent Locations •
All
Italy,
just now
UK,
1 minute ago
Australia,
1 minute ago
USA,
1 minute ago
Spain,
2 minutes ago
Norway,
3 minutes ago
United States,
4 minutes ago
Recent Awards •
All
Scholar
to
Devon Ryan
104k
Popular Question
to
blur
▴ 280
Popular Question
to
ATpoint
81k
Teacher
to
Haci
▴ 550
Popular Question
to
chevivien
▴ 90
Popular Question
to
Maxine
▴ 40
Popular Question
to
Shicheng Guo
★ 9.4k
Recent Replies
Comment: calculate mismatch rate from VCF file
by
Dora
▴ 10
Thank you for your reply!! My bad. I didn't mention that I want to get the mismatch rate for each site. Is this error rate for each site?
Comment: Interproscan taking so much time
by
dthorbur
★ 1.7k
Parallelize. Chunk your transcriptome into groups of something like 5000 (or less if you want it to go faster), and run an array across you…
Comment: Nanopore data filtering using fastp
by
dthorbur
★ 1.7k
Ah, sorry, I was thinking of the wrong command. You can either use `seqtk sample` or `seqkit sample`. I would recommend the former if your …
Comment: Variant calling of GBS data
by
analyst
▴ 10
It does not output warning when I skip flags for MQRankSum and ReadPosRankSum **java -jar -Xmx30G gatk.jar VariantFiltration -R reference…
Comment: Merging featureCounts output for different species
by
andrebolerbarros
• 0
Is there any list of homology you could use for this merging? Maybe this would be helpful
Comment: Variant calling of GBS data
by
Pierre Lindenbaum
160k
again, remove the spaces " "SOR > 10." -> " "SOR>10"
Comment: Variant calling of GBS data
by
analyst
▴ 10
It is still giving same warning java -jar -Xmx30G gatk.jar VariantFiltration -R reference.fa -V A_raw_snps.vcf -O A_filtered_snps.vcf --fi…
Comment: Nextflow ERROR : Timeout waiting for connection from pool
by
dzisis1986
▴ 70
It doesn't make sense how to change the threads and in my case it is not working! What kind of problem is that ? is it related to Amazon to…
Comment: STAR aligner options
by
theophile
• 0
I have finally found out the reason behind this behavior. As [pointed out by dsull][1], the beginning of the alignment of read1 to the rat…
Comment: Variant calling of GBS data
by
analyst
▴ 10
Right Pierre, thanks.
Comment: Variant calling of GBS data
by
Pierre Lindenbaum
160k
remove spaces in expressions. 'MQRankSum<0.4'
Comment: Variant calling of GBS data
by
analyst
▴ 10
![enter image description here][1] [1]: /media/images/710829f2-e4af-4743-a31d-822520b4
Comment: Variant calling of GBS data
by
analyst
▴ 10
Vcf file contains this information ![enter image description here][1] [1]: /media/images/b3f699e5-2dd9-4e08-8f5b-2a716544
Comment: Variant calling of GBS data
by
analyst
▴ 10
Command used : **java -jar -Xmx30G gatk.jar VariantFiltration -R reference.fa -V A_raw_snps.vcf -O A_filtered_snps.vcf --filter-name "QD_f…
Comment: Variant calling of GBS data
by
analyst
▴ 10
I am using gatK version 4.2.1.0 for variant filtration but it generates following warnings: 14:10:40.970 WARN JexlEngine - ![0,14]: 'Read…
Traffic: 2724 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6