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49 results • Page
1 of 1
Sort: Votes
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Votes
Replies
4
votes
2
replies
125
views
when I use htslib to write a bam. Error of "truncated file" shows by samtools
bam
htslib
10 minutes ago by
Aaron
▴ 10
3
votes
7
replies
2.3k
views
Tool:
Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
biomart
annotation
Ensembl
updated 8 hours ago by
Ram
44k • written 2.8 years ago by
Shred
★ 1.4k
3
votes
5
replies
165
views
I cannot download VG in any way
vg
vgteam
updated 9 hours ago by
GenoMax
142k • written 11 hours ago by
gforg34
▴ 10
3
votes
2
replies
213
views
vg autoindex seems stuck after a week of running
vg
pangenome
19 hours ago by
StevieP
▴ 10
3
votes
2
replies
158
views
How do i calculate the mean of triplicates in a data.frame based on pattern?
tidyverse
r
updated 18 hours ago by
zx8754
11k • written 1 day ago by
Assa Yeroslaviz
★ 1.9k
3
votes
6
replies
230
views
Best practices in Fungal Genome Assembly
illumina
assembly
nanopore
genome
5 hours ago by
Umer
▴ 50
3
votes
9
replies
1.5k
views
Rseqc infer_experiment.py: 0 usable reads sampled and unknown data type
rseqc
infer_experiment.py
RNA-seq
updated 2 hours ago by
mazegriff
• 0 • written 17 months ago by
pubsurfted
▴ 40
3
votes
3
replies
862
views
Cut&Run and heatmap
MACS2
bowtie2
updated 12 hours ago by
Ram
44k • written 13 months ago by
qudrat.nii
▴ 10
3
votes
12
replies
5.4k
views
7 follow
txt file to bigwig
MEME
bigwig
updated 12 hours ago by
GenoMax
142k • written 8.6 years ago by
tanni93
▴ 50
3
votes
7
replies
450
views
Z score
Z-score
updated 17 hours ago by
ATpoint
82k • written 5 days ago by
Akash D
▴ 60
2
votes
2
replies
213
views
Help me with Heatmap
RNA-seq
R
DESeq2
updated 18 hours ago by
zx8754
11k • written 1 day ago by
vmpsb
• 0
2
votes
2
replies
119
views
dbNSFP4.7a database format to Annovar Format?
snp
annovar
NGS
dbNSFP
updated 12 hours ago by
Ram
44k • written 21 hours ago by
Clark_BioMorgan
▴ 50
2
votes
1
reply
59
views
Intersection of multiple vcf files
isec
vcf
bcftools
updated 3 hours ago by
Jeremy Leipzig
22k • written 5 hours ago by
avelarbio46
▴ 30
2
votes
1
reply
229
views
Job:
2 PhD Students in single-cell bioinformatics
PhD
Genomics
single-cell
NGS
updated 3 hours ago by
Uzma
• 0 • written 5 days ago by
mtabaka
▴ 20
2
votes
7
replies
1.6k
views
Problems when trying to use ensembl-vep
ensembl
ensembl-vep
docker
updated 20 hours ago by
tomas4482
▴ 400 • written 10 months ago by
langziv
▴ 50
2
votes
3
replies
97
views
help in changing Y scale in R
ggplot2
R
updated 2 hours ago by
LauferVA
4.2k • written 5 hours ago by
Ghada
• 0
2
votes
1
reply
137
views
Is there any minimum number of counts in scRNAseq to consider that a gene is expressed?
scRNAseq
single-cell
seurat
scanpy
UMI
updated 15 hours ago by
ATpoint
82k • written 17 hours ago by
ev97
▴ 20
2
votes
2
replies
346
views
Annotating single cell data automatically
single-cell
updated 20 hours ago by
Nat.Nataren
▴ 20 • written 5 weeks ago by
Gerard
• 0
2
votes
3
replies
235
views
Search within posts based on tags using the Biostars API
api
meta
updated 12 hours ago by
Ram
44k • written 1 day ago by
Bálint
▴ 10
1
vote
2
replies
129
views
How do I check if a DNA sequence of a gene is supported by RNAseq data?
Genetics
RNA-seq
Phase-variation
Alignment
11 hours ago by
Jack
• 0
1
vote
0
replies
53
views
Why does WGCNA use weighted correlation instead of Pearson correlation?
wgcna
9 hours ago by
絶望燃やし
▴ 10
1
vote
9
replies
371
views
Error with pheatmap - 'from' must be a finite number
pheatmap
r
deseq2
updated 5 hours ago by
zx8754
11k • written 1 day ago by
vmpsb
• 0
1
vote
2
replies
184
views
How to Convert CNV Data to CNA Format for Reproducing Results with the Padma Package?
multi-omics
CNV
R
5 hours ago by
Ngrin
• 0
1
vote
2
replies
192
views
Salmon vs Kallisto vs RSEM
RSEM
quantification
kallisto
Salmon
19 hours ago by
Mohamed Abderrahmane
▴ 20
1
vote
2
replies
161
views
Polygenic Risk Score calculation
snp
polygene
prs
variants
15 hours ago by
ashaneev07
▴ 20
1
vote
3
replies
300
views
Failed to download data from EBI with ascp
EBI
aspera
updated 20 hours ago by
jude
• 0 • written 6 weeks ago by
biock
▴ 60
0
votes
2
replies
258
views
Tools for chromosomal aneuploidy detection
human-genetics
aneuploidy
NGS
updated 8 hours ago by
Ram
44k • written 5 days ago by
adarsh_pp
▴ 40
0
votes
0
replies
64
views
Regarding ENSEMBL/Gencode and UCSC differences (ATAC-seq, ChiPseeker peaks annotation)
ATAC-seq
CHiPseeker
Annotation
18 hours ago by
Manko47
• 0
0
votes
1
reply
168
views
finding highly divergent orthologs using exonerate
ortholog
Exonerate
evolution
updated 16 hours ago by
dthorbur
★ 2.0k • written 4 days ago by
Emily
▴ 20
0
votes
6
replies
538
views
How to build ribosomal interval files to use in CollectRnaSeqMetrics for hg38.p14
hg38.p14
ribosomal-intervals
15 hours ago by
naaj
• 0
0
votes
2
replies
158
views
Salmon ~ Effective Length
Salmon
updated 15 hours ago by
GenoMax
142k • written 1 day ago by
chrisk
• 0
0
votes
1
reply
160
views
Confirmation required on how DiffBind generates union of regions (min. 1bp overlap or gap)?
DiffBind
updated 14 hours ago by
GenoMax
142k • written 17 hours ago by
Ian
6.0k
0
votes
4
replies
700
views
Illumina EPIC v2 IlmnIDs and probe names
Illumina
EPIC
EPICv2
updated 12 hours ago by
Papyrus
★ 2.9k • written 6 months ago by
christine.a.pedersen
▴ 10
0
votes
4
replies
316
views
How to add Ensembl ids after Pseudobulk analysis by DESeq2
Seurat
Pseudobulk
single-cell
DESeq2
scRNA
updated 12 hours ago by
jared.andrews07
★ 17k • written 3 days ago by
Sara
▴ 30
0
votes
0
replies
72
views
Funcotator gnomAD incoherent number of output fields
gatk
gnomAD
Funcotator
updated 12 hours ago by
Ram
44k • written 1 day ago by
jaime alvarez
▴ 30
0
votes
0
replies
48
views
reference geome gaf file obsolent GO replacement
gaf
GO
11 hours ago by
Nicolas
• 0
0
votes
0
replies
117
views
virus genome annotation
annotation
gff3
consensus
NCBI
coding_regions
updated 8 hours ago by
Ram
44k • written 1 day ago by
Ghada
• 0
0
votes
0
replies
109
views
Subset of Transcripts- How do I proceed with it?
Stringtie
updated 8 hours ago by
Ram
44k • written 1 day ago by
Varsha
• 0
0
votes
0
replies
67
views
EXOME DEPTH - CNV
CNV
20 hours ago by
Neha
• 0
0
votes
1
reply
195
views
Facing problem with single cell rna seq annotation using singleR
singleR
scRNAseq
updated 7 hours ago by
Ram
44k • written 2 days ago by
sc_analysis
• 0
0
votes
0
replies
93
views
PyRMD
machine-learning
cheminformatics
Virtual-Screening
updated 7 hours ago by
Ram
44k • written 1 day ago by
s
• 0
0
votes
2
replies
244
views
How to decrease the motif score?
Motif-score
updated 7 hours ago by
Ram
44k • written 3 days ago by
Hadia
• 0
0
votes
2
replies
137
views
coding and non-coding region of the viral genome
viral-genome
7 hours ago by
Ghada
• 0
0
votes
0
replies
150
views
immuCell Abundance infiltrate
ImmuCell
updated 7 hours ago by
Ram
44k • written 3 days ago by
elbakri.fatimazahrae
• 0
0
votes
0
replies
56
views
NCBI vs Ensembl - Ortholog genes Information
Genomics
Orthologs
NCBI
Ensembl
updated 7 hours ago by
Pierre Lindenbaum
162k • written 7 hours ago by
José
▴ 10
0
votes
2
replies
217
views
Mutation counts corrected by number of samples
mutations
WES
genomics
WGS
6 hours ago by
garcesj
▴ 50
0
votes
0
replies
33
views
Using a within population reference genome - Recombination
relernn
vcf
popgen
recombination
6 hours ago by
dylan
• 0
0
votes
0
replies
15
views
monocle3 dot plot by groups and each cell types
monocle3
R
2 hours ago by
sooni
▴ 20
0
votes
1
reply
99
views
Can I count UMI-barcode combination without mapping?
HyDrop
protein
UMI
UMI-Tools
updated 51 minutes ago by
GenoMax
142k • written 11 hours ago by
Assa Yeroslaviz
★ 1.9k
49 results • Page
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Recent Votes
Answer: when I use htslib to write a bam. Error of "truncated file" shows by samtools
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
Comment: I cannot download VG in any way
Why does WGCNA use weighted correlation instead of Pearson correlation?
Explanation of vg deconstruct vcf output
I cannot download VG in any way
Comment: I cannot download VG in any way
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Recent Replies
Comment: when I use htslib to write a bam. Error of "truncated file" shows by samtools
by
Aaron
▴ 10
Thanks very much.
Answer: help in changing Y scale in R
by
LauferVA
4.2k
Hello @ab33b6d7 , Below is approximately the code block you provided, with a few additional lines added. Each of the new lines has > …
Comment: 2 PhD Students in single-cell bioinformatics
by
Uzma
• 0
I want to apply for this PhD position. I did MSc Zoology and MPhil biosciences.
Comment: Rseqc infer_experiment.py: 0 usable reads sampled and unknown data type
by
mazegriff
• 0
Hi pubsurfted, I ran into the same issue using a reference transcriptome with HISAT2 from the Ensembl database. For others with similar e…
Comment: Intersection of multiple vcf files
by
Jeremy Leipzig
22k
isec is pretty awful for these set operations - especially since individual samples present alleles, not lines in a VCF file. If you can co…
Comment: help in changing Y scale in R
by
Medhat
9.7k
Maybe try to calculate min and max combined_min <- min(a_filtered$value, a_filtered_tv$value, na.rm = TRUE) combined_max <- max(a_…
Answer: help in changing Y scale in R
by
ATpoint
82k
Use `+ylim(c(lower, upper))`. Either set manually, or query both `a_filtered` and `a_filtered_tv` for the minimum and maximum values that g…
Comment: Error with pheatmap - 'from' must be a finite number
by
zx8754
11k
I am not familiar with deseq data, but if it makes sense, remove rows/columns that have only NAs. #remove rows x<- mat.z[ rowSums(…
Answer: when I use htslib to write a bam. Error of "truncated file" shows by samtools
by
John Marshall
3.1k
There are several problems with this code: 1. You have not set `b->l_data`, which here should be set to the same value as `b->m_data`. T…
Comment: Best practices in Fungal Genome Assembly
by
Umer
▴ 50
Should I use both Recon and Pilon for polshing ? Recon uses Long-reads and Pilon uses short-read. if both should be used, is their any pref…
Comment: Mutation counts corrected by number of samples
by
garcesj
▴ 50
How come? If I have a pro-tumorigenic product, for example, wouldn't this comparison be valid?
Comment: How to Convert CNV Data to CNA Format for Reproducing Results with the Padma Pac
by
Ngrin
• 0
Thanks @Zhenyu Zhang for your response. I have just looked at the files you mentioned. Do you have any recommended package or code snippet …
Comment: coding and non-coding region of the viral genome
by
Ghada
• 0
As far I understand non coding region equal to the intergenic region? please can you write an example for how to calculate one region ? I…
Comment: How to Convert CNV Data to CNA Format for Reproducing Results with the Padma Pac
by
Zhenyu Zhang
★ 1.2k
In the GDC, there are raw float value CNV data, and integer CNV values after advanced modeling. If you only want those floating-point numbe…
Comment: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
by
Ram
44k
Please edit your original post and add this at the top so everyone reads that first. GeneCards politely asks people not to scrape - not res…
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