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113,889 results • Page
3 of 2278
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Votes
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0
votes
1
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164
views
The difference blastn output when using subject and db options
genome
blastn
mite
annotation
tracker
updated 3 days ago by
GenoMax
136k • written 3 days ago by
praasu
▴ 40
1
vote
3
replies
267
views
Identify clusters of populations based on gene expression
Seq
Single
cell
RNA
updated 3 days ago by
Nitin Narwade
★ 1.5k • written 3 days ago by
Bine
▴ 50
1
vote
7
replies
371
views
featureCounts results: low rate of 'Successfully assigned alignments'
FeatureCounts
HISAT2
RNA-seq
2 days ago by
Hamtaro
▴ 10
0
votes
1
reply
164
views
Python function to export the annotated records to genbank file using python and biopython
biopython
python
bioinformatic
programming
updated 3 days ago by
barslmn
★ 2.0k • written 3 days ago by
Saurabh
• 0
1
vote
6
replies
350
views
Discrepancy in total number of bases in trimmed read1 and read2 files after BBDuk
bbduk
2 days ago by
CTLong
▴ 20
2
votes
1
reply
161
views
unicycler error : [Errno 13] Permission denied:
unicycler
updated 3 days ago by
barslmn
★ 2.0k • written 3 days ago by
jiyoung
▴ 20
2
votes
4
replies
445
views
Protein Database
protein
course
database
updated 3 days ago by
Elisabeth Gasteiger
★ 2.3k • written 7 days ago by
Mery
• 0
0
votes
0
replies
101
views
Does breadth of coverage signify expression?
Coverage
breadth
Bedtools
Expression
count
3 days ago by
Smriti
▴ 10
0
votes
6
replies
295
views
I made an error when using metawrap to binning
metagenome
binning
metawrap
3 days ago by
alice005201314
• 0
1
vote
4
replies
271
views
Bowtie mapping for single_end read
bowtie
3 days ago by
Rita
• 0
0
votes
4
replies
184
views
MRI VBM issue
MRI
VBM
ROI
Rhesus
3 days ago by
Ethan Lee
• 0
5
votes
3
replies
277
views
SPAdes error: finished abnormally, OS return value: 21
SPAdes
updated 3 days ago by
Brian Bushnell
19k • written 3 days ago by
jiyoung
▴ 20
0
votes
5
replies
540
views
Lack of correspondance of GFA node IDs to giraffe/call node IDs
giraffe
pggb
vg
updated 3 days ago by
Wenhai
• 0 • written 6 weeks ago by
javierbelmor
• 0
0
votes
0
replies
107
views
missing region in the process of annotation
annotatr
minfi
3 days ago by
Aki
▴ 10
0
votes
3
replies
4.0k
views
pheatmap lengends are being cutoff
pheatmap
legends
rstudio
heatmaps
updated 3 days ago by
Chris S.
▴ 320 • written 2.7 years ago by
enh
• 0
0
votes
0
replies
334
views
Job:
Postdoctoral Researcher in Alzheimer's disease Genetics, Multi-Omics, and Imaging Biomarkers, St Louis, MO, USA
Multi-Omics
Imaging
Alzheimer
Genetics
4 days ago by
belloy
• 0
0
votes
2
replies
223
views
using RSEM with non Trinity assembly
SPAdes
Trinity
RSEM
4 days ago by
jen
• 0
0
votes
2
replies
320
views
Help doing differential expression analysis -experimental design and gProfiler TF interpretation-
gProfiler
mRNA
Differential-expression
TCGA
updated 2 days ago by
rajabolacuan
• 0 • written 10 days ago by
Camilo Andres
▴ 40
0
votes
1
reply
254
views
Diferences between TCGAbiolinks and cBioportal
R
TCGAbiolinks
cBioportal
updated 4 days ago by
Zhenyu Zhang
★ 1.1k • written 8 days ago by
jomagrax
▴ 40
1
vote
0
replies
100
views
Visualize and explore eventalign data against reference
igv
minimap
nanopolish
nanopore
ngs
4 days ago by
joe
▴ 390
0
votes
6
replies
373
views
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data?
RNA-Seq
Nanopore
ONT
differential
expression
2 days ago by
tw_140
• 0
3
votes
2
replies
198
views
Running STAR on fastq file generated from a RNA-seq experiment
STAR
RNAseq
fastq
files
updated 4 days ago by
Darked89
4.5k • written 4 days ago by
achanda
• 0
2
votes
3
replies
301
views
DEseq2 input
DEseq2
updated 4 days ago by
ATpoint
78k • written 4 days ago by
r.shiasi3897
▴ 10
0
votes
1
reply
165
views
Combine Geoids
Geoids
NCBI
updated 4 days ago by
ATpoint
78k • written 4 days ago by
anasjamshed
▴ 120
1
vote
2
replies
244
views
Best practices for unstranded sequences in featureCounts
featurecounts
overlapping
unstranded
3 days ago by
Enrique
• 0
1
vote
1
reply
188
views
Choose between pvalue & pvalue.adj
volcanoplot
updated 4 days ago by
Istvan Albert
99k • written 4 days ago by
Guitout
• 0
0
votes
5
replies
312
views
HTseq reports missing attribute name
htseq
updated 1 day ago by
Istvan Albert
99k • written 4 days ago by
Bjorn
• 0
3
votes
0
replies
159
views
Herald:
The Biostar Herald for Monday, November 27, 2023
herald
4 days ago by
Biostar
2.3k
9
votes
15
replies
784
views
Construction of single sequence assembly out of contigs
Contigs
Bacteria
Genome
WGS
3 days ago by
analyst
▴ 10
4
votes
2
replies
1.9k
views
Masurca. Failed to pre-correct Nanopore data, please check your data!
Nanopore
Masurca
updated 4 days ago by
colindaven
5.7k • written 2.4 years ago by
kamanovae
▴ 100
0
votes
0
replies
99
views
Differentiate sequenced and imputed variants in BGEN files
imputation
bgen
ukb
4 days ago by
user230613
▴ 350
0
votes
4
replies
271
views
Species coverage in the NCBI protein NR database ?
NR
updated 4 days ago by
Istvan Albert
99k • written 4 days ago by
HERMAN
▴ 10
0
votes
7
replies
424
views
Issues while running htseq-count
Candida-glabrata
RNA-seq
htseq-count
4 days ago by
Foad
▴ 10
0
votes
0
replies
107
views
addPatternDensity to qsea object
maxDensityPattern
medip
qsea
4 days ago by
Jaykishan
• 0
1
vote
1
reply
168
views
Harmony integration PC variance explained
scRNA
integration
harmony
updated 2 days ago by
CTLong
▴ 20 • written 4 days ago by
e.iich
• 0
0
votes
3
replies
239
views
merged rs number information
merged
dbsnp
3 days ago by
sskimvd
• 0
2
votes
1
reply
156
views
Bedtools intersection
bedtools
bed
intersect
vcf
updated 4 days ago by
Pierre Lindenbaum
158k • written 4 days ago by
rejoeraymond776
▴ 10
0
votes
2
replies
205
views
RnBeads mean difference vs M-values
Methylation
updated 4 days ago by
Basti
★ 1.9k • written 5 days ago by
a.basitkhan1990
▴ 30
1
vote
2
replies
185
views
RnBeads which p-value to use
Methylation
RnBeads
updated 5 days ago by
ATpoint
78k • written 5 days ago by
a.basitkhan1990
▴ 30
1
vote
1
reply
167
views
Beginner differential methylation analysis
Methylation
updated 4 days ago by
Basti
★ 1.9k • written 5 days ago by
a.basitkhan1990
▴ 30
4
votes
8
replies
580
views
Docker: Pass reads file form host to container
docker
4 days ago by
davidmaimoun
▴ 50
2
votes
1
reply
241
views
EnhancedVolcano underrepresenting DEGs
R
updated 3 days ago by
Kevin Blighe
86k • written 5 days ago by
jabbari.parnian
▴ 30
4
votes
5
replies
1.7k
views
PyMOL: Gaps in protein structure yet shown by the sequence
PyMOL
structure
protein
updated 5 days ago by
pippo1980
• 0 • written 9 months ago by
spence.lank
▴ 10
0
votes
0
replies
113
views
[maftools]Too many multi_hit and missense mutation
maftools
gatk
MAF
data
WES
VCF
5 days ago by
jiazheng_lin
• 0
0
votes
1
reply
186
views
multiple condition and time course in RNA-seq
edgeR
RNA-Seq
DESeq2
updated 4 days ago by
i.sudbery
18k • written 5 days ago by
tiancaigg
▴ 30
0
votes
0
replies
126
views
Negative F statistics for sex check in plink
plink
check
sex
5 days ago by
kl
▴ 10
2
votes
4
replies
326
views
Should SMART-seq2 data be deduplicated in STAR?
SMART-seq2
5 days ago by
anlinli.napert
• 0
0
votes
3
replies
375
views
Extracting list of identical items from several excel files
from
excel
items
Extract
file
updated 5 days ago by
DonPhager
• 0 • written 6 days ago by
otieno43
▴ 20
1
vote
2
replies
267
views
Indexing by bowtie2 but aligning with STAR
STAR
mm10
Bowtie2
Alignment
Index
5 days ago by
Anojan
• 0
0
votes
1
reply
195
views
Chipseq peak calling and peak frequency region
chipseeker
macs2
updated 4 days ago by
Arup Ghosh
3.2k • written 6 days ago by
Mehwish
▴ 10
113,889 results • Page
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Answer: GO categorization
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
Answer: GO categorization
C: Expected a file with 2 fields per line. GenomicsDBImport from GATK ?
C: Expected a file with 2 fields per line. GenomicsDBImport from GATK ?
Answer: Problematic fastq files...How can we trust them?
Comment: Problematic fastq files...How can we trust them?
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Answer: "MethylKit" package for WGBS data
by
viveksomya123
• 0
Why I am getting this histogram of CpG coverage using methylkit, is this the failure of bisulfite library preparation![enter image descript…
Comment: Should I scale all genes in single cell Seurat?
by
synat.keam
▴ 80
Thanks, António for your kind and detailed responses. You helped clear my doubt about scaling! Kind Regards, Synat
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
by
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19k
It's not a silly question! And yes, it can be done. JGI is currently testing various binning tools to try to find the best protocol for t…
Answer: GO categorization
by
geneontologyhelp
▴ 270
[We have this in our FAQ][1]. PANTHER version 18.0, which powers the enrichment analysis on our homepage, has [143 species][2] loaded and …
Comment: Problematic fastq files...How can we trust them?
by
blackadder
▴ 30
Thanks for the feedback fellas! I agree with the aforementioned!
Comment: Which program, tool, or strategy do you use to visualize genomic rearrangements?
by
cmdcolin
★ 3.4k
i collect a large list of tools for visualization, some are specialized for SVs and re-arrangements. you can filter by tag (SV, CNV, compar…
Answer: The number of variations in the pan-genome is reduced compared to the variations
by
Jordan M Eizenga
▴ 410
If variants overlap in the genome, `vg deconstruct` will combine them into one locus with multiple alleles. If your input VCF has a lot of …
Answer: How to find node Postion and source(sample) ?
by
Jordan M Eizenga
▴ 410
You can use `vg find -P` for this. This command is not really designed to be used frequently throughout the genome (each invocation loads t…
Comment: How Can I move the scattered dots more closer into the center of box ?
by
Brian Bushnell
19k
I would just draw them in by hand where you want them.
Comment: How to identify CG, CHG, or CHH from MeDIP data
by
Tm
★ 1.1k
I know that CpG types can be identified using whole genome bisulphite data. But could it be possible using MeDIP data too? We tried using Q…
Comment: Problematic fastq files...How can we trust them?
by
Brian Bushnell
19k
I'd have to agree there... while you can generally recover a fastq to the point that it is spec-compliant, you don't know how or why the f…
Answer: Finding human .vcf files online to download
by
cmdcolin
★ 3.4k
---------- some common ones include 1000 genomes vcf (large, multi-sample) http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ …
Comment: GO categorization
by
m.habib
• 0
Thanks Istvan for your reply. I think these programs will do the same as Trinotate. Trinotate searches against numerous databases and gener…
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp
by
jv
★ 1.2k
I wonder if using cell hashing, which would allow pooling of cells from multiple samples before droplet formation, could improve things her…
Comment: Where Can I Find The Basepair Positions Of Chromosome Bands?
by
Malachi Griffith
19k
And the hg38 version can be found here: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/cytoBand.txt.gz And for convenience, upda…
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