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606 results • Page
2 of 13
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2
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how to make a venn plot with data frame in R
plot
R
Venn
17 days ago by
satva72
• 0
4
votes
6
replies
545
views
How to pass from DNA to AA fasta
genetics
updated 16 days ago by
Buffo
★ 2.2k • written 19 days ago by
Anderson Stiward
• 0
2
votes
6
replies
646
views
How to identify the corresponding gene of a short sequence of a genome?
fasta
gene
genome
sequence
updated 1 day ago by
Ram
39k • written 3.5 years ago by
Kumar
▴ 100
4
votes
6
replies
1.5k
views
Why weblogo of biopython doesn't work?
Biopython
Weblogo
updated 5 days ago by
minakshiboruahassam
• 0 • written 9 months ago by
Plus
▴ 20
6
votes
6
replies
584
views
On "wings" in volcano plots...
DEG
volcano
DGE
statistics
DE
updated 19 days ago by
ATpoint
72k • written 20 days ago by
kalavattam
▴ 120
2
votes
6
replies
387
views
Find data-based Gene_IDs for unknown gene_IDs in gtf.file
RNA-SEQ
annotation
GO-term
17 days ago by
Pegasus
▴ 90
4
votes
6
replies
451
views
how to plot SV(structural variants) from many assemblies of a given locus
SV
21 days ago by
natalev
▴ 20
2
votes
6
replies
338
views
Embryo transcriptome
database
transcriptome
SRA
updated 7 hours ago by
Basti
★ 1.6k • written 2 days ago by
firefox91
• 0
0
votes
6
replies
342
views
variant allelic fraction
vep
updated 1 day ago by
Ram
39k • written 3 days ago by
Jom
• 0
3
votes
6
replies
1.1k
views
how to get total read count, mapped read count and unmapped read count from multiple sam or bam files
RNAseq
PYTHON
R
bash
updated 22 days ago by
Ram
39k • written 2.7 years ago by
Bioinfonext
▴ 430
3
votes
5
replies
1.3k
views
Trouble with best practices
samtools
WES
NGS
GATK
updated 19 days ago by
Ram
39k • written 5.3 years ago by
erarroji
• 0
0
votes
5
replies
1.5k
views
terminal can't activate base automatically (conda)
conda
updated 27 days ago by
Ram
39k • written 22 months ago by
Binghong
▴ 20
0
votes
5
replies
852
views
trimmomatic unknown trimmer
Trimmomatic
updated 23 days ago by
Ram
39k • written 20 months ago by
Xiaoyun
▴ 10
0
votes
5
replies
711
views
vcftools --weir-fst-pop returns -nan
fst
vcftools
updated 8 days ago by
mingxi
• 0 • written 5 months ago by
elizabeth
• 0
0
votes
5
replies
391
views
how to Construct a Newick tree file from five large fasta files
tree
Newick
alignment
updated 5 days ago by
Joe
21k • written 5 days ago by
gunala.nikhil
• 0
2
votes
5
replies
390
views
RNA SEQ reads assembly for illumina sequenced data
NGS
linux
nanopore
updated 28 days ago by
Ram
39k • written 5 weeks ago by
Adyasha
• 0
0
votes
5
replies
2.0k
views
error during installationi of KisSplice
cpp
c
RNA-Seq
kissplice
SNP
updated 16 days ago by
Ram
39k • written 6.8 years ago by
yoyofangliu
• 0
0
votes
5
replies
511
views
get allele frequency (MAF) value from snp
biomaRt
MAF
ensembl
SNP
R
25 days ago by
Barista
• 0
0
votes
5
replies
955
views
bigwigs to reads in peaks
R
atac-seq
updated 5 hours ago by
Ram
39k • written 2.4 years ago by
pt.taklifi
▴ 60
0
votes
5
replies
361
views
Problem with GPU guppy_basecaller and SLURM
nanopore
guppy
updated 15 days ago by
Medhat
9.6k • written 15 days ago by
kenneditodd
▴ 10
0
votes
5
replies
597
views
Making disjoint chromosomal sites contiguous with awk
awk
assembly
bash
sequence
updated 19 days ago by
Ram
39k • written 2.6 years ago by
selplat21
▴ 20
1
vote
5
replies
1.3k
views
WGCNA Co-expression network analysis on cuffdiff output
wgcna
cuffdiff
updated 14 days ago by
Ram
39k • written 4.7 years ago by
sbb
▴ 10
1
vote
5
replies
2.3k
views
Calculating distance matrix of RNA-seq data
Dynamic-Time-Warping
R
time-series
updated 8 days ago by
Ram
39k • written 5.2 years ago by
fi1d18
★ 4.2k
0
votes
5
replies
416
views
combine/merge closet variants into one from mutect2
variants
mutect2
merge
gatk
updated 23 days ago by
Istvan Albert
98k • written 28 days ago by
J.F.Jiang
▴ 900
3
votes
5
replies
432
views
STAR error with a loop
STAR
RNA
transcriptomics
updated 27 days ago by
Ram
39k • written 6 months ago by
luzglongoria
▴ 40
0
votes
5
replies
951
views
Bioinformatics conference with possible publication
conference
updated 13 days ago by
Ram
39k • written 4.7 years ago by
bharata1803
▴ 550
0
votes
5
replies
3.1k
views
Phylogeny Heatmap with Python
multiple-sequence-alignment
updated 22 days ago by
Ram
39k • written 4.2 years ago by
marina.gerges
• 0
1
vote
5
replies
539
views
kraken on nt library
kraken
nt
15 days ago by
Francois Piumi
▴ 30
1
vote
5
replies
3.6k
views
Time-series or pairwise comparison EdgeR - what's more suited?
DGE-analysis
Time-series
pairwise
updated 8 days ago by
Ram
39k • written 6.8 years ago by
Biogeek
▴ 470
0
votes
5
replies
69
views
VCF file CSQ flag
vcf
exome-sequencing
updated 1 hour ago by
Ram
39k • written 3 hours ago by
Payal
▴ 140
5
votes
5
replies
1.6k
views
bio-newbie / gene research / tools and methods
methods
research
gene
updated 20 days ago by
Ram
39k • written 5.4 years ago by
wizofe
• 0
2
votes
5
replies
418
views
Cutadapt error: too many parameters.
cutadapt
parallel
bash
8 days ago by
DanielEB_fisk
▴ 10
2
votes
5
replies
444
views
How to check a gene in an open chromatin region or not?
ATAC-seq
29 days ago by
Chris
▴ 100
3
votes
5
replies
362
views
Uniprot API access to download .pdb files
PDB
API
Python
Uniprot
14 days ago by
jdrohan
• 0
0
votes
5
replies
807
views
Read DNA sequence from FASTA rising a subclass?
FASTA
python
updated 19 days ago by
Ram
39k • written 2.6 years ago by
Gonçalo
• 0
4
votes
5
replies
1.2k
views
Distributed / parallel computing in bioinformatics
distributed-computing
updated 23 days ago by
Ram
39k • written 5.9 years ago by
CY
▴ 710
0
votes
5
replies
1.4k
views
Best Blast Hits from Tabular Outputs in Multiple files
python
shell
blast
updated 21 days ago by
Ram
39k • written 5.7 years ago by
trini1god
• 0
0
votes
4
replies
294
views
I need help with a methyl array data analysis
methyl_array
DMPs
DMRs
beta_value
r
10 days ago by
Ahmad
▴ 10
1
vote
4
replies
962
views
Simulate the sequence data
next-gen-sequencing
genetics
updated 16 days ago by
Ram
39k • written 5.1 years ago by
bha
▴ 80
3
votes
4
replies
230
views
retaining only the clusters of interest
seurat
single-cell
scRna-seq
updated 8 hours ago by
Ram
39k • written 1 day ago by
shamza
• 0
0
votes
4
replies
350
views
desgin a primer for CDS
gene
pcr
11 days ago by
yuxiang
• 0
0
votes
4
replies
370
views
What are recommended parameters for the local protein alignment ?
protein
alignment
3 days ago by
Alexander
▴ 70
1
vote
4
replies
362
views
Pre-processing for Agilent microarray data?
affymetrix
microarray
gene
agilent
rna
updated 10 days ago by
solarchan7
• 0 • written 15 days ago by
survive
• 0
1
vote
4
replies
2.3k
views
Using a Multiple Seq Alignment tool for pairwise alignments possible?
multiple-sequence-alignment
msa
alignment
updated 22 days ago by
Ram
39k • written 7.1 years ago by
nchuang
▴ 260
12
votes
4
replies
504
views
Annotating TSS: By Transcript or by Gene? Code Validation Help Needed!
genome
bed
transcript
TSS
23 days ago by
Rafael Soler
★ 1.2k
0
votes
4
replies
1.6k
views
Extra header column stopping EMMAX (C), but not seen in input files
emmax
genomics
Cpp
plink
GWAS
updated 16 days ago by
Ram
39k • written 5.3 years ago by
michael.nagle
▴ 100
4
votes
4
replies
360
views
Segmentation fault Biopython pairwise alignment
biopython
alignment
updated 8 days ago by
Joe
21k • written 12 days ago by
antoine.fauchois92
▴ 20
2
votes
4
replies
1.4k
views
Gettin Consensus From Multiple Whole Genomes
multiple-sequence-alignment
whole-genome-alignment
updated 22 days ago by
Ram
39k • written 6.4 years ago by
nilaylale88
• 0
2
votes
4
replies
823
views
Downloading all the heteroComplex protein PDB IDs in RCSB Protein Data Bank
python
biopython
updated 2 days ago by
Ram
39k • written 3.6 years ago by
Christian
• 0
0
votes
4
replies
698
views
blast engine error empty blast query vector
Blast
alignment
updated 27 days ago by
Ram
39k • written 4 months ago by
Sowmya Pulapet
▴ 30
606 results • Page
2 of 13
Recent Votes
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
A: Mouse promoter regions
Answer: How to get information about promoter from bulk-RNAseq?
A: Extracting Flanking Regions across TSS using R scripts
A: Mouse promoter regions
A: Finding zebrafish promoters ENSEMBL
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Comment: How to get information about promoter from bulk-RNAseq?
by
camillab.
▴ 130
and what about enhancer? is it possible to do it from a bulk-RNAseq?
Comment: How to get information about promoter from bulk-RNAseq?
by
camillab.
▴ 130
yes! clearly the terminology on my side needs to improved!
Comment: How to get information about promoter from bulk-RNAseq?
by
rpolicastro
12k
Generally speaking, most promoters only initiate transcription for a single gene, with a single gene potentially having multiple promoters …
Answer: How to get information about promoter from bulk-RNAseq?
by
Trivas
★ 1.2k
I'd probably select the genes of interest from your bulk RNA-seq results then use the UCSC table browser to get the sequence upstream of th…
Comment: How to add annotation columns with specific colors to the heatmap?
by
Ram
39k
Show us your exact code - it is quite easy to tweak colors in ComplexHeatmap with the `col=` argument.
Comment: VCF file CSQ flag
by
Ram
39k
True, but it's not technically impossible to annotate GVCFs, which is why I did not address that point.
Comment: Creating a local version of Clustered NR database
by
PeterC_NCBI
▴ 260
@genomax Sorry for the delay in reply. We're still working out the details of what exactly to provide. One idea is to provide just the rep…
Comment: Shannon's Entropy by Sliding Window in R
by
rohitsatyam102
▴ 690
Hi Were u able to achieve this?
Comment: Differences in GTF files hg19 and hg38
by
GenoMax
130k
Since this is not an answer to the original question do not add it as such. I moved your last comment to the correct spot it should have be…
Comment: VCF file CSQ flag
by
Pierre Lindenbaum
154k
if your talking about the gvcf produced by HaplotypeCaller with ERC=GVCF, you don't annote g.vcf files , you must first merge the g.vcf.f…
Comment: [python]sklearn.ensemble.RandomForestClassifier(TypeError: string indices must b
by
Ram
39k
https://www.biostars.org/u/127538/ : Please delete this question or it will be deleted by moderators in a few days.
Comment: VCF file CSQ flag
by
Ram
39k
A gvcf files has blocks for both variant loci and non-variant loci, so you won't see a CSQ for each record, only for those variant loci wit…
Comment: Differences in GTF files hg19 and hg38
by
heureuse
• 0
Thank you very much. I get it from UCSC.
Comment: [python]sklearn.ensemble.RandomForestClassifier(TypeError: string indices must b
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Arup Ghosh
3.2k
This post does not fit the theme of this forum.
Comment: CellRanger problem
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3.2k
Try with atleast 32 GB of Memory rather than 16 GB specified by `limitGenomeGenerateRAM` option.
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