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19,549 results • Page
1 of 391
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0
votes
1
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34
views
which statistical test and which package for comapre datasets?
R
package
statistical
test
updated 39 minutes ago by
Jeremy
▴ 860 • written 2 hours ago by
satva72
• 0
0
votes
2
replies
59
views
Is interleaved Fastq files the same as interlaced fastq
manipulation
Data
updated 2 hours ago by
rpolicastro
12k • written 2 hours ago by
RCMC
• 0
10
votes
6
replies
4.8k
views
How to create interval list from reference fasta or dict file?
GATK
updated 6 hours ago by
Manuel Sokolov Ravasqueira
▴ 100 • written 2.9 years ago by
MatthewP
★ 1.3k
773
votes
164
replies
129k
views
107 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 9 weeks ago by
Biostar
2.3k • written 7.0 years ago by
Istvan Albert
99k
0
votes
5
replies
115
views
GetPileupSummaries intervals-list with Targeted Sequencing?
Variant-Calling
Somatic
intervals.bed
GetPileUpSummaries
GATK
updated 1 hour ago by
Pierre Lindenbaum
158k • written 7 hours ago by
Manuel Sokolov Ravasqueira
▴ 100
0
votes
0
replies
44
views
Test for multiplicative effect in mendelian randomization?
R
mendelian_randomization
GWAS
8 hours ago by
clairvoyant
• 0
0
votes
1
reply
95
views
Is GeSeq currently unavailable?
GeSeq
updated 9 hours ago by
GenoMax
136k • written 10 hours ago by
zy
• 0
0
votes
0
replies
65
views
Cibersort input data
cibersort
12 hours ago by
Maryam
• 0
0
votes
4
replies
361
views
using RSEM with non Trinity assembly
SPAdes
Trinity
RSEM
updated 5 days ago by
Dunois
★ 2.4k • written 12 days ago by
jen
• 0
0
votes
1
reply
915
views
How to run Aracne cytoscape plugin ?
R
software error
rna-seq
updated 18 hours ago by
gentlemonster
• 0 • written 3.2 years ago by
prithvi.mastermind
▴ 50
0
votes
0
replies
78
views
Tutorials for Spatial Transcriptomics
ST-Seq
Scanpy
Seurat
19 hours ago by
saqlain
▴ 90
0
votes
2
replies
143
views
autodock vina on mac
docking
mgltools
virtualbox
5 hours ago by
iamsmor
• 0
0
votes
1
reply
133
views
How can I obtain the DNA sequences of each CDS for several genbank files?
genbank
DNA
sequence
updated 20 hours ago by
Ram
41k • written 1 day ago by
Raphaëlle
• 0
0
votes
1
reply
125
views
identifying SNPs from short read sequencing data
Sequencing
updated 17 hours ago by
GenoMax
136k • written 21 hours ago by
reaset41
• 0
0
votes
0
replies
136
views
Transcript Assembly for Multiple Species Using StringTie and Orthogroup Discovery using OrthoFinder
Species
StringTie
Orthogroups
Transcript
Assembly
21 hours ago by
dtnondorf
• 0
0
votes
1
reply
126
views
Java class error message when using BBDuk
rna-seq
bbduk
updated 17 hours ago by
GenoMax
136k • written 22 hours ago by
milewski
• 0
0
votes
0
replies
83
views
how to run the compare_genomes for comparative analysis
genome
orthofinder
evolution
22 hours ago by
rj.rezwan
• 0
2
votes
8
replies
1.9k
views
7 follow
LCA from BLAST output
lca
blast
updated 5 hours ago by
Dunois
★ 2.4k • written 3.1 years ago by
makrez
▴ 50
0
votes
0
replies
81
views
Infer ancestry for RNA-seq data
plink
admixture
ancestry
updated 23 hours ago by
Ram
41k • written 23 hours ago by
Matthew Chang
• 0
1
vote
3
replies
201
views
CIGAR and query sequence lengths differ
pysam
samtools
21 hours ago by
ManuelDB
▴ 80
0
votes
3
replies
170
views
GO, KEGG, GSEA analysis with ~5 DEGs
GO
KEGG
updated 23 hours ago by
Istvan Albert
99k • written 1 day ago by
foejvs546
▴ 10
5
votes
3
replies
223
views
Rstudio cloud
R
single-cell
21 hours ago by
synat.keam
▴ 80
0
votes
0
replies
73
views
Apply BSQR for Targeted Sequencing
GenomicPipelines
GATK
variant-calling
23 hours ago by
Manuel Sokolov Ravasqueira
▴ 100
0
votes
1
reply
119
views
WGCNA Dendrogram Branch missing from modules
WGCNA
dendrogram
hdWGCNA
updated 7 hours ago by
andres.firrincieli
3.5k • written 23 hours ago by
mhale
• 0
0
votes
1
reply
112
views
Bowtie 2 alignment
Bowtie2
updated 23 hours ago by
Ram
41k • written 1 day ago by
Elizabeth
▴ 30
0
votes
0
replies
71
views
bcftools=1.18 not filtering correcting MAF
bcftools
minor-allele-frequency
VCF
updated 20 hours ago by
Ram
41k • written 1 day ago by
AMARU
• 0
1
vote
1
reply
125
views
How to subtract variants from one VCF file to another?
joint-genotyping
vcf
variant-calling
gatk
updated 1 day ago by
Pierre Lindenbaum
158k • written 1 day ago by
cee28
▴ 30
0
votes
1
reply
132
views
Alternative to Gentrome?
salmon
updated 17 hours ago by
GenoMax
136k • written 1 day ago by
yee
• 0
0
votes
0
replies
74
views
Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
Gene-Expression
DESeq2
updated 1 day ago by
Ram
41k • written 1 day ago by
aehall26
• 0
16
votes
4
replies
401
views
6 follow
Forum:
What Are The Most Influential Bioinformatics/Computational Biology Papers Of 2023?
genomics
snps
survey
papers
updated 1 day ago by
Ram
41k • written 1 day ago by
Raony Guimarães
★ 1.4k
0
votes
0
replies
79
views
Finding differentially expressed genes between Seurat clusters
Seurat
updated 1 day ago by
Ram
41k • written 1 day ago by
Bine
▴ 50
0
votes
0
replies
75
views
JoinLayers function for Seurat Object for annotation with SingleR
Seurat
updated 1 day ago by
Ram
41k • written 1 day ago by
Bine
▴ 50
0
votes
0
replies
87
views
Error: Failed to open /ROH/.log. Try changing the --out parameter.
plink
ROH
1 day ago by
sevda
• 0
1
vote
5
replies
230
views
Normalization of RNA captureSeq data (<20 genes captured)
captureSeq
edgeR
DESeq2
RNA
ERCC
updated 1 day ago by
ATpoint
78k • written 1 day ago by
jips
• 0
1
vote
1
reply
152
views
How to properly mock a (Pysam) read
pysam
updated 23 hours ago by
Istvan Albert
99k • written 1 day ago by
ManuelDB
▴ 80
3
votes
3
replies
246
views
How to avoid missannotated GO terms?
swissprot
GO
enrichment
updated 1 day ago by
Elisabeth Gasteiger
★ 2.3k • written 2 days ago by
Dr.Animo
▴ 80
2
votes
6
replies
274
views
gatk SelectVariants is giving duplicate allele error while extracting SNPs out of vcf file
SNP
variant-calling
gatk
updated 1 day ago by
Ram
41k • written 1 day ago by
analyst
▴ 10
1
vote
2
replies
183
views
Where to download excel file to include major human disease, prevalence and incidence?
Disease
Burden
updated 1 day ago by
GenoMax
136k • written 1 day ago by
Shicheng Guo
★ 9.3k
0
votes
0
replies
95
views
how to label Histological regions on the H&E images in 10x visium H&E images
spatial-transcriptome
updated 1 day ago by
Ram
41k • written 1 day ago by
naodaigua_weng
• 0
0
votes
0
replies
100
views
Converting txt.gz to PLINK bim
S-LDSC
file
LDSC
format
1 day ago by
X
• 0
2
votes
2
replies
211
views
how to draw the valcano plot for DEGs in a different way
valcano
plot
DEGs
updated 23 hours ago by
Ram
41k • written 1 day ago by
luckyday1661
• 0
0
votes
3
replies
214
views
SQL request from NCBI metadata and stat_analysis tables
SQL
NCBI
BigQuery
1 day ago by
marie.harmel
• 0
0
votes
1
reply
158
views
get gene name from rsID
dbSNP
updated 1 day ago by
Ram
41k • written 2 days ago by
a3532321
• 0
2
votes
2
replies
934
views
fgsea leading edge genes
gsea
updated 1 day ago by
Ram
41k • written 2.3 years ago by
charlielonergan
▴ 20
3
votes
4
replies
229
views
how to remove multiple columns from a file in R
r
1 day ago by
Bioinfonext
▴ 440
0
votes
3
replies
203
views
Convert NCBI Downloaded files to ANNOVAR format
ANNOVAR
updated 1 day ago by
Ram
41k • written 1 day ago by
robert
• 0
0
votes
0
replies
102
views
Confusing results from FindConservedMarkers in Seurat
10XGenomics
1 day ago by
pm2012
▴ 140
0
votes
5
replies
281
views
Differential expression using Bowtie2
Transcriptome
Bowtie
Differential-expression
updated 1 day ago by
ATpoint
78k • written 2 days ago by
8d8fc19e
• 0
1
vote
5
replies
348
views
Read count vs Depth
Bedtools
updated 18 hours ago by
Brian Bushnell
20k • written 2 days ago by
Mary
• 0
0
votes
0
replies
104
views
use GEOparse to download series supplemental files?
gse
geoparse
python
geoquery
geo
2 days ago by
mk
▴ 290
19,549 results • Page
1 of 391
Recent Votes
Comment: GATK GetPileupSummaries Java heap space
Answer: How to subtract variants from one VCF file to another?
What Are The Most Influential Bioinformatics/Computational Biology Papers Of 2023?
What Are The Most Influential Bioinformatics/Computational Biology Papers Of 2023?
Answer: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 202
Answer: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 202
Answer: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 202
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Recent Replies
Comment: which statistical test and which package for comapre datasets?
by
Jeremy
▴ 860
I think you will need at least three replicates to be able to do statistics.
Comment: GetPileupSummaries intervals-list with Targeted Sequencing?
by
Pierre Lindenbaum
158k
> Asking for bed file is not a suitable option in the current scenario. ???????
Comment: GetPileupSummaries intervals-list with Targeted Sequencing?
by
Manuel Sokolov Ravasqueira
▴ 100
they only provided me the sorted.bam files aligned with hg19. I converted bam into fastq and started variant calling from there. Asking for…
Comment: GetPileupSummaries intervals-list with Targeted Sequencing?
by
Pierre Lindenbaum
158k
> kit is proprietary I can't imagine you get a targeted sequencing without having a BED file....
Comment: GetPileupSummaries intervals-list with Targeted Sequencing?
by
Manuel Sokolov Ravasqueira
▴ 100
thanks for the suggestion. how can i obtain the bedfile of my targets (kit is proprietary - can I obtain bed from fasta? if yes how?)
Comment: Is interleaved Fastq files the same as interlaced fastq
by
rpolicastro
12k
This may indicate that your R1 and R2 reads were processed in a way that didn't maintain the 1:1 order of matching forward and reverse read…
Comment: Is interleaved Fastq files the same as interlaced fastq
by
RCMC
• 0
Sorry I accidentally hit enter BWA-MEM2 has occurring some error and states that paired reads have different names so I am trying to com…
Comment: GetPileupSummaries intervals-list with Targeted Sequencing?
by
Pierre Lindenbaum
158k
how about using the bed file of your targets....
Answer: LCA from BLAST output
by
Dunois
★ 2.4k
You should probably be using `MMseqs2`'s `taxonomy` module for this: [https://github.com/soedinglab/MMseqs2#taxonomy][1] . [1]: https:/…
Comment: autodock vina on mac
by
iamsmor
• 0
thank you but ı am already follow this tutorial steps but at mgltools steps at the page but ı dont undertsand there isnot no enough explana…
Comment: How to create interval list from reference fasta or dict file?
by
Manuel Sokolov Ravasqueira
▴ 100
Hello @MatthewP , were you able to that for a fasta file for example? If you have a fasta file containing a targeted region, how to you ge…
Comment: WGCNA Dendrogram Branch missing from modules
by
andres.firrincieli
3.5k
I am not familiar with hdWGCNA but perhaps some modules are excluded because their genes are not expressed in a certain proportion of cells.
Comment: LCA from BLAST output
by
Michael
53k
If you know the lineage information is complete you could compare which columns are identical, however, there may be unranked levels in bet…
Comment: Is GeSeq currently unavailable?
by
GenoMax
136k
Email the developers listed on contact page: https://chlorobox.mpimp-golm.mpg.de/contact.html
Comment: Alternative to Gentrome?
by
GenoMax
136k
Curious as to what is `gentrome`? Genome decoy + transcriptome?
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