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 : today
all time
today
this week
this month
this year
45 results • Page
1 of 1
Sort: Votes
Rank
Views
Votes
Replies
7
votes
17
replies
1.3k
views
Building reference dbSNP file using WGS samples
NGS
WGS
Variant-calling
non-model
Bootstrapping
2 hours ago by
analyst
▴ 10
6
votes
4
replies
1.3k
views
Effect of Bootstrapping/Gibbs Sampling in Salmon Counts
Gibbs
Bootstrapping
RNAseq
Salmon
Sampling
updated 15 hours ago by
Gordon Smyth
★ 6.5k • written 18 months ago by
saipra003
▴ 10
5
votes
4
replies
281
views
How to query 1000 genomes project VCF files for specific regions without downloading whole chromosomes first?
r
ensembl
dataslicer
vcf
1000genomes
updated 21 minutes ago by
Pierre Lindenbaum
158k • written 1 day ago by
kilojarek
▴ 10
4
votes
9
replies
6.3k
views
6 follow
Merge two bigwig(+/- strand) files from RNA-seq
RNA-Seq
next-gen
sequencing
updated 17 hours ago by
rls_08
▴ 40 • written 6.5 years ago by
izzy.yichao.cai
▴ 180
4
votes
6
replies
2.0k
views
How to do simple pathway analysis?
rna-seq
genome
gene
updated 19 hours ago by
he1k
• 0 • written 4.6 years ago by
Seq225
▴ 110
2
votes
2
replies
205
views
How to add exon annotations to genome annotation
proteome
genome
BED
annotation
17 hours ago by
Simone
▴ 10
2
votes
4
replies
171
views
how to remove multiple columns from a file in R
r
4 hours ago by
Bioinfonext
▴ 440
2
votes
4
replies
193
views
convert dataframe R
R
updated 22 hours ago by
Ram
41k • written 23 hours ago by
satva72
• 0
2
votes
6
replies
204
views
gatk SelectVariants is giving dupilicate allele error while extracting SNPs out of vcf file
SNP
variantcalling
gatk
3 hours ago by
analyst
▴ 10
2
votes
5
replies
639
views
Genome coverage of MAGs while submitting to NCBI
genome
MAGs
coverage
metagenomics
updated 18 hours ago by
Mensur Dlakic
★ 25k • written 3 months ago by
Konstantin
• 0
2
votes
2
replies
887
views
fgsea leading edge genes
gsea
updated 16 hours ago by
Ram
41k • written 2.3 years ago by
charlielonergan
▴ 20
1
vote
1
reply
43
views
Normalization of RNA captureSeq data (<20 genes captured)
captureSeq
edgeR
DESeq2
RNA
ERCC
updated 2 hours ago by
ATpoint
78k • written 2 hours ago by
jips
• 0
1
vote
4
replies
245
views
Read count vs Depth
Bedtools
7 hours ago by
Mary
• 0
1
vote
4
replies
181
views
select unique samples in R
statistics
r
biostatistics
updated 22 hours ago by
bk11
★ 1.8k • written 1 day ago by
Bioinfonext
▴ 440
1
vote
1
reply
113
views
recommend gene ranking methods when doing GSEA
Gene_rank
GSEA
updated 20 hours ago by
rpolicastro
12k • written 22 hours ago by
luckyday1661
• 0
1
vote
6
replies
270
views
Multi-factor designs in DiffBind
Chipseq
Multi-factor
Diffbind
updated 18 hours ago by
Rory Stark
★ 2.0k • written 1 day ago by
g.persic1991
• 0
1
vote
10
replies
550
views
Where is the index command?
samtools
updated 21 hours ago by
jkbonfield
★ 1.2k • written 8 days ago by
luque007
• 0
1
vote
0
replies
23
views
What Are The Most Influential Bioinformatics/Computational Biology Papers Of 2023?
snps
bioinformatics
survey
papers
genomics
updated 32 minutes ago by
Michael
53k • written 37 minutes ago by
Raony Guimarães
★ 1.3k
1
vote
3
replies
272
views
Genetic data QC prior to imputation
imputation
updated 23 minutes ago by
Raony Guimarães
★ 1.3k • written 13 days ago by
kl
▴ 10
0
votes
3
replies
184
views
How to avoid missannotated GO terms?
swissprot
GO
enrichment
updated 5 hours ago by
Elisabeth Gasteiger
★ 2.3k • written 22 hours ago by
Dr.Animo
▴ 80
0
votes
2
replies
142
views
Opinion on miRNA pipeline
miRNA
pipeline
4 hours ago by
ju_ra
• 0
0
votes
2
replies
107
views
Where to download excel file to include major human disease, prevalence and incidence?
Disease
Burden
updated 4 hours ago by
GenoMax
136k • written 6 hours ago by
Shicheng Guo
★ 9.3k
0
votes
0
replies
41
views
How to properly mock a (Pysam) read
pysam
2 hours ago by
ManuelDB
▴ 80
0
votes
0
replies
31
views
Error: Failed to open /ROH/.log. Try changing the --out parameter.
plink
ROH
2 hours ago by
sevda
• 0
0
votes
3
replies
132
views
SQL request from NCBI metadata and stat_analysis tables
SQL
NCBI
BigQuery
1 hour ago by
marie.harmel
• 0
0
votes
5
replies
163
views
Differential expression using Bowtie2
Transcriptome
Bowtie
Differential-expression
updated 32 minutes ago by
ATpoint
78k • written 19 hours ago by
8d8fc19e
• 0
0
votes
0
replies
56
views
Converting txt.gz to PLINK bim
S-LDSC
file
LDSC
format
11 hours ago by
X
• 0
0
votes
0
replies
147
views
Outgroup for 1000 genomes project
haplotype
1000Genomes
phylogeny
updated 22 hours ago by
Ram
41k • written 4 months ago by
Morgan
• 0
0
votes
3
replies
155
views
Consensus peaksets in DiffBind - conceptual questinos
DiffBind
updated 22 hours ago by
Rory Stark
★ 2.0k • written 23 hours ago by
Sam
▴ 300
0
votes
0
replies
203
views
Haplotype network/phylogeny of 1000 genomes project
haplotype
1000Genomes
phylogeny
updated 22 hours ago by
Ram
41k • written 5 months ago by
Morgan
• 0
0
votes
1
reply
484
views
FASTQ files for 30x 1KGP of Phase 3 data
1000genomes
fastq
updated 21 hours ago by
Ram
41k • written 13 months ago by
Qboy
• 0
0
votes
1
reply
105
views
Does orthofinder allow more than one proteome per species as input ?
comparative-genomics
orthology
updated 22 hours ago by
Ram
41k • written 1 day ago by
Sara
• 0
0
votes
1
reply
143
views
scRNA data analysis , how to compare pattern in multiple samples
R
scRNA
updated 21 hours ago by
Ram
41k • written 1 day ago by
Confused_human
▴ 20
0
votes
0
replies
76
views
how to run GSEA with spesific background
RNA-seq
GSEA
updated 21 hours ago by
Ram
41k • written 1 day ago by
Chava
• 0
0
votes
2
replies
968
views
RPKM on TSS using DiffBind
RPKM
TSS
DiffBind
updated 21 hours ago by
Ram
41k • written 2.4 years ago by
g.persic1991
• 0
0
votes
2
replies
200
views
Aligning sequences with multiple genetic codes!
genetic_codes
codon
MEGA11
alignment
updated 20 hours ago by
pippo1980
• 0 • written 2 days ago by
George X.
• 0
0
votes
0
replies
61
views
News:
New version of ElasticBLAST (1.2.0) available from NCBI
ElasticBLAST
NCBI
BLAST
20 hours ago by
PeterC_NCBI
▴ 370
0
votes
0
replies
65
views
use GEOparse to download series supplemental files?
gse
geoparse
python
geoquery
geo
19 hours ago by
mk
▴ 290
0
votes
0
replies
64
views
Confusing results from FindConservedMarkers in Seurat
10XGenomics
18 hours ago by
pm2012
▴ 140
0
votes
1
reply
112
views
get gene name from rsID
dbSNP
updated 16 hours ago by
Ram
41k • written 19 hours ago by
a3532321
• 0
0
votes
2
replies
154
views
How to perform quality control for sex when there are no variants after thresholding for MAF
sex
check
genetics
15 hours ago by
kl
▴ 10
0
votes
3
replies
148
views
Convert NCBI Downloaded files to ANNOVAR format
ANNOVAR
updated 15 hours ago by
Ram
41k • written 18 hours ago by
robert
• 0
0
votes
3
replies
232
views
Curated model organism gene functional annotations
Interpro
C.elegans
GO-terms
updated 23 hours ago by
manaswwm
▴ 490 • written 1 day ago by
ian.will
▴ 10
0
votes
1
reply
112
views
how to draw the valcano plot for DEGs in a different way
valcano
plot
DEGs
updated 9 hours ago by
CTLong
▴ 30 • written 14 hours ago by
luckyday1661
• 0
0
votes
0
replies
52
views
how to label Histological regions on the H&E images in 10x visium H&E images
region
transcriptome
label
spatial
8 hours ago by
naodaigua_weng
• 0
45 results • Page
1 of 1
Recent Votes
Comment: Normalization of RNA captureSeq data (<20 genes captured)
What Are The Most Influential Bioinformatics/Computational Biology Papers Of 2023?
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out
Answer: How to query 1000 genomes project VCF files for specific regions without downloa
Answer: Issue softclipping reads when they belong and don't belong to a common amplicon
Answer: Issue softclipping reads when they belong and don't belong to a common amplicon
Answer: how to remove multiple columns from a file in R
Recent Locations •
All
Germany,
just now
United States,
just now
Netherlands,
just now
Lebanon,
2 minutes ago
Dublin / Ireland,
3 minutes ago
London,
3 minutes ago
France,
3 minutes ago
Recent Awards •
All
Centurion
to
Raony Guimarães
★ 1.3k
Scholar
to
Trivas
★ 1.5k
Rising Star
to
analyst
▴ 10
Scholar
to
aw7
▴ 230
Teacher
to
Pierre Lindenbaum
158k
Popular Question
to
MatthewP
★ 1.3k
Popular Question
to
Shicheng Guo
★ 9.3k
Recent Replies
Comment: How to query 1000 genomes project VCF files for specific regions without downloa
by
Pierre Lindenbaum
158k
run a `system()` command from R ?
Comment: Genetic data QC prior to imputation
by
Raony Guimarães
★ 1.3k
Check how many variants you have without filtering for MAF, maybe use a MAF of 0.01? You could try the --impute-sex **ycount** or **y-only*…
Comment: Differential expression using Bowtie2
by
ATpoint
78k
> What would you do if you wanted to compare differential expression of a gene across tissues from RNA-seq data? Get a dataset that has ev…
Comment: How to query 1000 genomes project VCF files for specific regions without downloa
by
kilojarek
▴ 10
Thanks @Pierre this is great to know, although it doesn't solve my issue of this being R-self-contained. rsamtools doesn't seem to carry fu…
Comment: Differential expression using Bowtie2
by
8d8fc19e
• 0
Ok, thanks for letting me know. What would you do if you wanted to compare differential expression of a gene across tissues from RNA-seq da…
Comment: SQL request from NCBI metadata and stat_analysis tables
by
marie.harmel
• 0
To put it more simply with another example, I try to display every possible order for every phyla founded in my run but I don't find the l…
Comment: SQL request from NCBI metadata and stat_analysis tables
by
marie.harmel
• 0
Thank you for your answer but unfortunately I tried it and it makes the same kind of ouptut as mine, with multtiple new (false) lines (spl…
Comment: Normalization of RNA captureSeq data (<20 genes captured)
by
ATpoint
78k
What is the question exactly? With only 20 genes you basically **must** use the spike-ins as that few genes do not really allow to normaliz…
Comment: Building reference dbSNP file using WGS samples
by
analyst
▴ 10
Dear [Brian][1] I realized that problem is with callvariants.sh script because when I called variants using freebayes I did not find aforem…
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out
by
analyst
▴ 10
Its bbmap tool callvariants.sh. I think you are right because I did not get such error when I called variants through freebayes.
Answer: Efficient way of calculating the number of mismatches between two sets of sequen
by
j.gleixner
• 0
Since all your sequences have the same length (say M) and you are only looking concerned with hamming distance you can encode your sequence…
Comment: Where to download excel file to include major human disease, prevalence and inci
by
GenoMax
136k
ChatGPT says Disease Prevalence Approximate Number of Cases (Worldwide) Cardiovascular Diseases High Over 17 million deaths annual…
Comment: Where to download excel file to include major human disease, prevalence and inci
by
Pierre Lindenbaum
158k
using wikidata: https://query.wikidata.org/sparql?query=%0ASELECT%20%3Fitem%20%3FitemLabel%20%3FitemDescription%20%3Fprevalence%20%3Fdoid%0…
Comment: Opinion on miRNA pipeline
by
ju_ra
• 0
Thank you very much! I see you decided to go for Bowtie as aligner. Do you see any issue in using STAR (as a splice aware reader technicall…
Answer: How to avoid missannotated GO terms?
by
Elisabeth Gasteiger
★ 2.3k
Please contact the UniProt helpdesk whenever you find such annotations, especially in these cases where the GO evidence/source tag says "Un…
Traffic: 2069 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