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525 results • Page
2 of 11
Sort: replies
Rank
Views
Votes
Replies
0
votes
5
replies
488
views
get allele frequency (MAF) value from snp
biomaRt
MAF
ensembl
SNP
R
18 days ago by
Barista
• 0
0
votes
5
replies
697
views
vcftools --weir-fst-pop returns -nan
fst
vcftools
updated 1 day ago by
mingxi
• 0 • written 5 months ago by
elizabeth
• 0
2
votes
5
replies
438
views
How to check a gene in an open chromatin region or not?
ATAC-seq
22 days ago by
Chris
▴ 100
0
votes
5
replies
393
views
combine/merge closet variants into one from mutect2
variants
mutect2
merge
gatk
updated 16 days ago by
Istvan Albert
98k • written 21 days ago by
J.F.Jiang
▴ 900
0
votes
5
replies
325
views
Problem with GPU guppy_basecaller and SLURM
nanopore
guppy
updated 8 days ago by
Medhat
9.6k • written 8 days ago by
kenneditodd
▴ 10
3
votes
5
replies
1.3k
views
Trouble with best practices
samtools
WES
NGS
GATK
updated 12 days ago by
Ram
39k • written 5.3 years ago by
erarroji
• 0
0
votes
5
replies
841
views
trimmomatic unknown trimmer
Trimmomatic
updated 16 days ago by
Ram
39k • written 20 months ago by
Xiaoyun
▴ 10
5
votes
5
replies
1.6k
views
bio-newbie / gene research / tools and methods
methods
research
gene
updated 13 days ago by
Ram
39k • written 5.4 years ago by
wizofe
• 0
1
vote
5
replies
1.3k
views
WGCNA Co-expression network analysis on cuffdiff output
wgcna
cuffdiff
updated 7 days ago by
Ram
39k • written 4.7 years ago by
sbb
▴ 10
0
votes
5
replies
1.4k
views
terminal can't activate base automatically (conda)
conda
updated 20 days ago by
Ram
39k • written 21 months ago by
Binghong
▴ 20
0
votes
5
replies
3.1k
views
Phylogeny Heatmap with Python
multiple-sequence-alignment
updated 15 days ago by
Ram
39k • written 4.2 years ago by
marina.gerges
• 0
0
votes
5
replies
2.0k
views
error during installationi of KisSplice
cpp
c
RNA-Seq
kissplice
SNP
updated 9 days ago by
Ram
39k • written 6.8 years ago by
yoyofangliu
• 0
0
votes
5
replies
1.4k
views
Best Blast Hits from Tabular Outputs in Multiple files
python
shell
blast
updated 14 days ago by
Ram
39k • written 5.6 years ago by
trini1god
• 0
0
votes
5
replies
454
views
Splitting heatmap
R
updated 23 days ago by
Papyrus
★ 2.5k • written 25 days ago by
hafiz.talhamalik
▴ 350
0
votes
5
replies
946
views
Bioinformatics conference with possible publication
conference
updated 6 days ago by
Ram
39k • written 4.7 years ago by
bharata1803
▴ 550
0
votes
5
replies
595
views
Making disjoint chromosomal sites contiguous with awk
awk
assembly
bash
sequence
updated 12 days ago by
Ram
39k • written 2.6 years ago by
selplat21
▴ 20
2
votes
5
replies
388
views
Cutadapt error: too many parameters.
cutadapt
parallel
bash
1 day ago by
DanielEB_fisk
• 0
0
votes
5
replies
804
views
Read DNA sequence from FASTA rising a subclass?
FASTA
python
updated 12 days ago by
Ram
39k • written 2.6 years ago by
Gonçalo
• 0
3
votes
5
replies
347
views
Uniprot API access to download .pdb files
PDB
API
Python
Uniprot
7 days ago by
jdrohan
• 0
2
votes
5
replies
383
views
RNA SEQ reads assembly for illumina sequenced data
NGS
linux
nanopore
updated 21 days ago by
Ram
39k • written 4 weeks ago by
Adyasha
• 0
1
vote
5
replies
2.3k
views
Calculating distance matrix of RNA-seq data
Dynamic-Time-Warping
R
time-series
updated 1 day ago by
Ram
39k • written 5.2 years ago by
fi1d18
★ 4.2k
4
votes
5
replies
1.2k
views
Distributed / parallel computing in bioinformatics
distributed-computing
updated 16 days ago by
Ram
39k • written 5.9 years ago by
CY
▴ 710
1
vote
5
replies
510
views
kraken on nt library
kraken
nt
8 days ago by
Francois Piumi
▴ 30
3
votes
4
replies
2.4k
views
Unable to install Autogrid4
autogrid
software-error
autogrid4
updated 14 days ago by
Ram
39k • written 2.2 years ago by
roybatty269
• 0
1
vote
4
replies
808
views
R package error messages have missing package names
R
updated 16 days ago by
Ram
39k • written 20 months ago by
Rahul Tyagi
• 0
0
votes
4
replies
3.7k
views
What is Dunn's multiple comparison test?
statistics
updated 15 days ago by
Ram
39k • written 5.7 years ago by
Koreanraichu
• 0
0
votes
4
replies
858
views
bowtie2 -all ... multiple alignment Chip-seq
bowtie2
alignment
ChIP-Seq
multiple-alignment
updated 15 days ago by
Ram
39k • written 3.6 years ago by
poltora4enko
▴ 10
0
votes
4
replies
324
views
csv to custom manifest file
illumina
20 days ago by
bioguy24
▴ 230
1
vote
4
replies
364
views
Bacterial metatransciptome antimicrobial resistance genes workflow?
RNAseq
metatranscriptomics
14 days ago by
SushiRoll
▴ 100
0
votes
4
replies
274
views
How do I add row names to pheatmap() when I am using a pre-normalized matrix?
pheatmap
heatmap
rna-seq
updated 5 days ago by
Trivas
★ 1.1k • written 6 days ago by
mgranada3
• 0
0
votes
4
replies
1.1k
views
No space separating sequence and name PopArt error !?
popart
traits
haplotypes
python
updated 19 days ago by
Ram
39k • written 2.0 years ago by
matache.razvan911
• 0
3
votes
4
replies
1.3k
views
fastPHASE -F provided to estimate haplotype frequencies, but no freqs in output
genomics
phasing
fastPHASE
updated 9 days ago by
Ram
39k • written 5.2 years ago by
lakemonster
▴ 10
1
vote
4
replies
2.3k
views
Using a Multiple Seq Alignment tool for pairwise alignments possible?
multiple-sequence-alignment
msa
alignment
updated 15 days ago by
Ram
39k • written 7.1 years ago by
nchuang
▴ 260
1
vote
4
replies
265
views
My VCF file structure is strange and less compatible to data processing programs.
VCF
GATK
SNPs
updated 21 days ago by
Istvan Albert
98k • written 21 days ago by
kgwkk2
• 0
5
votes
4
replies
1.5k
views
Detection of DE genes among different tissues of an organism during time - RNA seq
detection
DE-genes
multi-treatments
time-series
updated 1 day ago by
Ram
39k • written 6.9 years ago by
statfa
▴ 720
0
votes
4
replies
4.8k
views
Sequence alignment length
multiple-sequence-alignment
updated 15 days ago by
Ram
39k • written 6.3 years ago by
biobudhan
▴ 20
1
vote
4
replies
4.8k
views
Conditionally coloring the fold change values to plot a heatmap using pheatmap
R
heatmap
updated 12 days ago by
Ram
39k • written 5.2 years ago by
chetana
▴ 60
4
votes
4
replies
336
views
Segmentation fault Biopython pairwise alignment
biopython
alignment
updated 1 day ago by
Joe
21k • written 5 days ago by
antoine.fauchois92
▴ 20
0
votes
4
replies
319
views
SCT transform
scttranform
seurat
updated 27 days ago by
ATpoint
72k • written 28 days ago by
No.Lar037477
▴ 10
1
vote
4
replies
548
views
What statistical test to apply for DE after CibersortX deconvolution
cibersortx
differential-expression
t-test
deconvolution
updated 19 days ago by
ATpoint
72k • written 4 weeks ago by
Sam
▴ 280
1
vote
4
replies
2.5k
views
DBD::mysql::st execute failed: The table 'InplgOrthoInplg
orthomcl
ortho
ubuntu
mysql
updated 7 days ago by
Ram
39k • written 5.0 years ago by
wocana
▴ 20
12
votes
4
replies
493
views
Annotating TSS: By Transcript or by Gene? Code Validation Help Needed!
genome
bed
transcript
TSS
16 days ago by
Rafael Soler
★ 1.2k
0
votes
4
replies
476
views
BBduk reading fastq from S3 directly - Is it possibile?
BBduk
BBTools
BBMap
10 days ago by
Marko
▴ 10
0
votes
4
replies
264
views
I need help with a methyl array data analysis
methyl_array
DMPs
DMRs
beta_value
r
3 days ago by
Ahmad
▴ 10
0
votes
4
replies
325
views
desgin a primer for CDS
gene
pcr
4 days ago by
yuxiang
• 0
1
vote
4
replies
344
views
Pre-processing for Agilent microarray data?
affymetrix
microarray
gene
agilent
rna
updated 3 days ago by
solarchan7
• 0 • written 8 days ago by
survive
• 0
2
votes
4
replies
1.3k
views
hisat2 SyntaxError: invalid syntax
alignment
hisat2
updated 16 days ago by
Ram
39k • written 19 months ago by
Xiaoyun
▴ 10
3
votes
4
replies
629
views
R package DESeq2 in R 3.5.1
R
updated 20 days ago by
Ram
39k • written 4 months ago by
sehriban.buyukkilic
• 0
1
vote
4
replies
100
views
Filter VCF file for variant alleles
VCF
variants
bcftools
vcftools
updated 1 hour ago by
Ram
39k • written 4 hours ago by
miguellarrazlopezdenovales
• 0
0
votes
4
replies
785
views
Detecting Biomarkers from Time Series Gene Epression data
Time-Series
Gene-Expression
Biomarkers
updated 1 day ago by
Ram
39k • written 3.1 years ago by
donnieDarko
• 0
525 results • Page
2 of 11
Recent Votes
Problem with PGDSpider v 2.1.0.2
Comment: Filter VCF file for variant alleles
Help making ADMIXTURE output digestible
Answer: Graphing Average Expression of Group of Genes
Linear models with limma: coefficients not estimatable, are the others OK?
Answer: How to find gene annotation given a position in a bacterial genome
Comment: INSTALLING DEseq2 via conda
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Recent Replies
Comment: Problem with PGDSpider v 2.1.0.2
by
sackettl
▴ 20
I have this same problem with version 2.1.1.5. Did you ever find a solution?
Comment: Filter VCF file for variant alleles
by
Ram
39k
> can't find anything to do this It's in there. If you had looked a little deeper, you would have found - on your own - exactly what Pierr…
Comment: To call variants can I use my aligned WGS data as a reference genome
by
GenoMax
129k
Then create an alternate Reference with data for the sample: https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateR…
Comment: Help making ADMIXTURE output digestible
by
Aaron
▴ 10
You can also check out [pong][1] (README [here][2]), which creates interactive plots with the clusters and colors automatically aligned acr…
Comment: To call variants can I use my aligned WGS data as a reference genome
by
mls
• 0
Yes they are but I wanna compare one of my samples with others , rather S288C.
Comment: To call variants can I use my aligned WGS data as a reference genome
by
Pierre Lindenbaum
154k
the bam are mapped on S288C fasta isn't it ? why would you need another reference ?
Comment: Filter VCF file for variant alleles
by
Pierre Lindenbaum
154k
use a filtering expression https://samtools.github.io/bcftools/bcftools.html#expressions , something like; bcftools view -i 'COUNT(GT=…
Comment: Filter VCF file for variant alleles
by
miguellarrazlopezdenovales
• 0
I've tried bcftools, which seems to be the closest I've got, but I can't find anything to do this. I have also found vcftools --max-non-ref…
Comment: Filter VCF file for variant alleles
by
Ram
39k
What have you tried? You've mentioned bcftools as a tag, have you read the manual?
Comment: How to concatenate multiple fasta file
by
doggie
• 0
@shenwei356 Thank you so much! Your prompt reply helped me a lot!
Answer: PacBio Pipeline and Tools for Variant Call
by
William Rowell
▴ 250
> What are Quality parameters that should be taken care ( Adapter trim, Reads filter, Min Data size, ) How to trim adapter, What tools to u…
Comment: Ambient RNA expression correction
by
rpolicastro
12k
Ambient RNA would have the same cell barcode as a valid cell-containing droplet since the RNA gets partitioned into the droplet with the ce…
Comment: Can any one suggest tools that generate "mind-maps" on concepts in biology/biote
by
Vincent Laufer
★ 2.8k
sorry to be blunt but this question is so broad i worry it may not evoke a cogent answer. you might start by finding a review on the use …
Answer: Can any one suggest tools that generate "mind-maps" on concepts in biology/biote
by
Jesse
▴ 550
Haven't used it, but I've heard good things about [Obsidian](https://obsidian.md/) as a note-taking tool, and it has [graphing features](ht…
Comment: How to concatenate multiple fasta file
by
shenwei356
8.1k
Another common way: 1. Split by isolates $ seqkit split --id-regexp "^(.+)_[\w\.]+:.+" --by-id-prefix "" -i merged.fa -O tmp --f…
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