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32 results • Page
1 of 1
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3
votes
11
replies
2.0k
views
What is NCBI Gene ID, where to find it and how to convert to entrez ID?
RNA-Seq
updated 3 hours ago by
GenoMax
129k • written 3.6 years ago by
mnazir
▴ 10
4
votes
7
replies
2.2k
views
low bootstrap value?
phylogeny
genome
alignment
updated 19 hours ago by
Ram
39k • written 4.0 years ago by
Kumar
▴ 100
0
votes
6
replies
126
views
The inchworm process failed. Trinity running error.
inchworm
transcriptome
trinity
updated 2 hours ago by
GenoMax
129k • written 8 hours ago by
Marta
• 0
1
vote
4
replies
178
views
Filter VCF file for variant alleles
VCF
variants
bcftools
vcftools
updated 20 hours ago by
Ram
39k • written 22 hours ago by
miguellarrazlopezdenovales
• 0
1
vote
3
replies
151
views
How to get a comperative result of 2 bed files?
bam
cnv
bed
updated 9 hours ago by
Pierre Lindenbaum
154k • written 1 day ago by
herh
• 0
0
votes
3
replies
164
views
minimap's SAM file MAPQ value for the unique alignments
minimap
MAPQ
RNAseq
6 hours ago by
Mohd
• 0
0
votes
3
replies
118
views
My kernel is killing the pairtools dedup script, how to prevent that?
ubuntu
hic
pairtools
aws
updated 3 hours ago by
GenoMax
129k • written 11 hours ago by
NikhilP
▴ 20
0
votes
3
replies
111
views
DEGseq for multiple samples
DEGseq
DEG
updated 3 hours ago by
Ram
39k • written 8 hours ago by
ALOUSH ALI
• 0
2
votes
3
replies
1.2k
views
mutational signatures in different tumor samples
somatic mutation
mutational signature
updated 1 hour ago by
Vincent Laufer
★ 2.9k • written 4.4 years ago by
lzy
▴ 20
1
vote
3
replies
162
views
To call variants can I use my aligned WGS data as a reference genome
VCF
samtools
reference
genome
updated 20 hours ago by
GenoMax
129k • written 20 hours ago by
mls
• 0
0
votes
2
replies
132
views
readGenericHeader() error message Limma
rna
limma
microarray
genomics
normalization
15 hours ago by
survive
• 0
0
votes
2
replies
143
views
Ambient RNA expression correction
scRNAseq
SoupX
Seurat
updated 23 hours ago by
rpolicastro
12k • written 1 day ago by
Pac314
▴ 10
0
votes
2
replies
519
views
1-way-2-fold cross family analysis
cross-family-analysis
updated 23 hours ago by
Ram
39k • written 3.8 years ago by
sinha.shriprakash
▴ 20
1
vote
1
reply
3.1k
views
Problem with PGDSpider v 2.1.0.2
alignment
updated 19 hours ago by
sackettl
▴ 20 • written 6.9 years ago by
maria.segovia.ramirez
▴ 10
0
votes
1
reply
1.2k
views
Best tool for bacterial genomic island prediction?
genome
genomic-island
updated 23 hours ago by
Ram
39k • written 4.0 years ago by
Kumar
▴ 100
0
votes
1
reply
88
views
how to look for interactions between different chromosomes
SNP
interactions
Gene
HiC
updated 2 hours ago by
Buffo
★ 2.2k • written 22 hours ago by
rheab1230
▴ 140
1
vote
1
reply
1.6k
views
Bioinformatics tools for Plasmid detection
short-read
plasmid
updated 1 hour ago by
Ram
39k • written 3.9 years ago by
El Niño
▴ 10
0
votes
1
reply
77
views
bioinformatic analysis protocol performed by CD Genomics
Genomics
CD
analysis
bioinformatic
Protocol
updated 9 hours ago by
barslmn
★ 1.5k • written 13 hours ago by
linnet.roque6
▴ 10
0
votes
0
replies
180
views
What are the existing proposals for how to approach genomic coordinates in a pangenome reference environment?
coordinates
pangenome
genomic
13 hours ago by
Vincent Laufer
★ 2.9k
0
votes
0
replies
76
views
Tool to align metagenomic data to reference genome
tool
metagenomics
alignment
22 hours ago by
Maddie
• 0
0
votes
0
replies
78
views
snpEff error. No CDS checked
snpEff
gtf
WES
22 hours ago by
fifty_fifty
▴ 40
1
vote
0
replies
85
views
Linear models with limma: coefficients not estimatable, are the others OK?
limma
21 hours ago by
fr
▴ 200
0
votes
0
replies
80
views
Help with running ATAC using Encode pipeline
encode
ATAC-seq
20 hours ago by
Chris
▴ 100
0
votes
0
replies
72
views
Determining Cutoff for score in a bed file in ATAC-seq Data Analysis
bed
ATAC-seq
updated 20 hours ago by
Ram
39k • written 20 hours ago by
Mah
• 0
0
votes
0
replies
61
views
PRSice-2 using SNPs with extremely low P-value
PRSice-2
SNP
16 hours ago by
Apprentice
▴ 140
0
votes
0
replies
66
views
RRBS fastq - biased per base sequence content
fastqc
rrbs
15 hours ago by
mbk0asis
▴ 660
0
votes
0
replies
62
views
Pore-C-Snakemake output files
contacts
23 hours ago by
oksana03fel
• 0
1
vote
0
replies
36
views
Considering gaps in calculating conservation score from MSA
multiple
alignment
sequence
conservation
python
4 hours ago by
Jonathan Lefebre
▴ 50
0
votes
0
replies
31
views
How to detect specific genes in metagenomics data
detection
metagenomics
genes
updated 4 hours ago by
GenoMax
129k • written 4 hours ago by
aziznasr1920
• 0
0
votes
0
replies
38
views
Metabolomics Data Annotation
annotation
metabolomics
camera
updated 2 hours ago by
Ram
39k • written 9 hours ago by
Rishabh Jha
• 0
0
votes
0
replies
30
views
Combination of ROC CURVE
roccurve
R
AUC
2 hours ago by
Maria17
▴ 10
0
votes
0
replies
466
views
Do we still really need to remove the sequence (Protein or Genome) redundancy when using deep learning approaches to construct prediction models?
sequence-redundancy
updated 2 hours ago by
Ram
39k • written 3.9 years ago by
kurdt325
• 0
32 results • Page
1 of 1
Recent Votes
Considering gaps in calculating conservation score from MSA
Comment: ggsave() bug in ggplot2?
Comment: How to calculate kinship matrix table from vcf file
including samples for which group is unknown to help adjust for another variable
Comment: including samples for which group is unknown to help adjust for another variable
Answer: ggsave() bug in ggplot2?
Comment: ggsave() bug in ggplot2?
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Recent Replies
Comment: BioInformatics, Software
by
Vincent Laufer
★ 2.9k
biostars.org is a great website for that
Answer: BioInformatics, Software
by
Jesse
▴ 560
Here's a couple that are geared toward hands-on bioinformatics learning: * [rosalind.info](https://rosalind.info) * [sandbox.bio](htt…
Comment: ggsave() bug in ggplot2?
by
Medeea
• 0
Yes, ggsave("Figure1.pdf") works very good as well!
Comment: How GATK pipeline called a homozygeous alternate allele (1/1) although one copy
by
Jeremy Leipzig
21k
> So how GATK called this ref allele if there is no reads supporting it it didn't call it reference. it called it hom_alt. where in your f…
Comment: mutational signatures in different tumor samples
by
Vincent Laufer
★ 2.9k
as far as im concerned, thats a recommendation not a disclaimer
Comment: including samples for which group is unknown to help adjust for another variable
by
Vincent Laufer
★ 2.9k
Actually, I just remembered the perfect paper to illustrate that idea. Look at this: https://pubmed.ncbi.nlm.nih.gov/35976223/. In this man…
Comment: including samples for which group is unknown to help adjust for another variable
by
Vincent Laufer
★ 2.9k
yep! updated my answer to respond to this. i think they ARE biological variables. it is understanding the nature of those variables that is…
Answer: ggsave() bug in ggplot2?
by
Medeea
• 0
I think the issue is solved with saving the file as .png There must be a problem with the .jpg format then. Thanks everyone for the va…
Comment: ggsave() bug in ggplot2?
by
Ram
39k
Try PDF. You won't need dpi for that. Also, do things work well if you use the lower level `png(); ggplot(); dev.off();` sequence instead o…
Comment: How to calculate kinship matrix table from vcf file
by
chrchang523
10k
The last vcftools release was in 2018. It has been superseded by bcftools for most purposes, and by plink 1.9/2.0 for most analytical func…
Comment: NarrowPeak format -Peak field
by
ATpoint
72k
I do not follow, can you please add a chr-start-end example.
Comment: BioPython: convert fasta to fastq without quality score input file
by
capemaster
• 0
The command with `gawk` is: awk 'BEGIN {RS = ">" ; FS = "\n"} NR > 1 {print $1"\n"$2"\n+\n"gensub(/./, "I", "g", $2)}'
Comment: The inchworm process failed. Trinity running error.
by
GenoMax
129k
So with 600M reads you will need a minimum of 600GB of RAM per trinity recommendations. If you are not able to get more memory consider no…
Comment: How GATK pipeline called a homozygeous alternate allele (1/1) although one copy
by
Ram
39k
I don't understand what you're saying. Your allele is different from the ref allele so it needs the sample to support that? Why? Give me t…
Comment: How GATK pipeline called a homozygeous alternate allele (1/1) although one copy
by
mohsamir2016
▴ 30
Sure, but n my case 1/1 the allel is different from the reference allele and it called it as T, for instance. So it needs reads in the samp…
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