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122,198 results • Page
640 of 2444
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0
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0
replies
790
views
Analysis of CRISPR screening with very strong positive selection
MAGeCK
CRISPR
4.5 years ago by
di4mond
• 0
0
votes
1
reply
1.7k
views
Build phylogenetic tree with alignment file
nwk
phylogenetic
aln
alignment
updated 4.5 years ago by
Michael
56k • written 4.5 years ago by
Jonathan Yoou
▴ 70
0
votes
0
replies
1.2k
views
Job:
PhD scholarship in bioinformatics in Rostock (Baltic Coast), Germany
aging
nutrition
updated 4.4 years ago by
Ram
45k • written 4.5 years ago by
Daniel Palmer
• 0
0
votes
1
reply
1.3k
views
How do I correctly add a plasmid sequence with multiple genes to a gtf as well as fasta file?
gtf
fasta
plasmid
updated 4.5 years ago by
Arsenal
▴ 160 • written 4.5 years ago by
a.wa
• 0
7
votes
4
replies
2.3k
views
Up to date bulk RNA-seq Quality Control tools?
QC
RNA-seq
4.5 years ago by
Pratik
★ 1.1k
0
votes
4
replies
1.4k
views
AWS EC2 connection with External hard drive (portable hard drive)
EC2
AWS
updated 4.4 years ago by
Ram
45k • written 4.5 years ago by
eunbi9561
• 0
0
votes
1
reply
1.2k
views
samtools mpileup: error CRC32 failure
sequencing
SNP
genome
next-gen
gene
updated 4.5 years ago by
Pierre Lindenbaum
166k • written 4.5 years ago by
lz1903
▴ 10
1
vote
1
reply
859
views
Finding if genes present in a gene list intersect genomic intervals
bed
encode
gene
4.0 years ago by
alexmondaini
▴ 20
0
votes
1
reply
2.2k
views
Packages installation: Permission denied
bioconductor
R
packages
updated 4.5 years ago by
zx8754
12k • written 4.5 years ago by
Zineb
▴ 10
1
vote
2
replies
971
views
Split a sam file by chromosome
CNVs
NGS
PRISM
updated 4.5 years ago by
GenoMax
154k • written 4.5 years ago by
ICfc97
▴ 20
4
votes
6
replies
2.9k
views
Trim bam file reads to the same length
RNA-Seq
genome
sequencing
next-gen
updated 4.5 years ago by
Juke34
9.3k • written 5.8 years ago by
rrapopor
▴ 40
0
votes
0
replies
821
views
Job:
Postdoc position on Modeling Gene Disruptions involved in Speech and Language Impairment in Human Neurons
transcriptomics
single
epigenetics
cell
4.5 years ago by
pancakeplant
▴ 10
1
vote
2
replies
2.7k
views
Salmon quant produced an error
Salmon
Linux
updated 22 months ago by
Muffin Man
▴ 10 • written 4.5 years ago by
Mohamed Samir
▴ 30
2
votes
1
reply
1.1k
views
effects of posttranslational protein modifications database?
post-translational-modification
protein
updated 15 months ago by
Ram
45k • written 4.5 years ago by
Camelia
▴ 30
0
votes
1
reply
1.7k
views
bcftools add AD column
ad
bcftools
vcf
updated 4.5 years ago by
zx8754
12k • written 4.5 years ago by
martina.gallinaro
• 0
1
vote
5
replies
2.6k
views
Trimmomatic: Unknown trimmer error
fastq
trimmomatic
RNA-seq
4.5 years ago by
foxiw
▴ 10
0
votes
0
replies
1.7k
views
Job:
Research Assistant in the Systems Environmental Microbiology Group at DTU Biosustain
engineering
Strain
4.4 years ago by
info
▴ 90
1
vote
1
reply
992
views
CNV in EPIC Illumina DNA methylation
bed
CNV
Conumee
updated 2.7 years ago by
Ram
45k • written 4.5 years ago by
NS
• 0
4
votes
4
replies
3.0k
views
awk, count and print the number of lines following a separator then add value of header to that column
awk
updated 4.5 years ago by
zx8754
12k • written 4.5 years ago by
Tash
▴ 20
1
vote
2
replies
1.8k
views
FastQC report of the metagenomic data
Metagenomics
Microbiome
WholeShotgunMetagenome
FastQC
Data-Analysis
4.5 years ago by
serene.s
• 0
0
votes
1
reply
1.0k
views
copy number variation and aneuploidy
aneuploidy
number
copy
variation
updated 4.5 years ago by
German.M.Demidov
★ 3.0k • written 4.5 years ago by
GG
• 0
0
votes
4
replies
1.8k
views
Getting biological replicates from SRA run NCBI
fastq
AWS
SRA
RNAseq
20 months ago by
Andres
▴ 20
0
votes
1
reply
1.5k
views
Forum:
Opinions on SLAM-Seq for Differential Gene Analysis
DGE
RNA-Seq
htseq
updated 4.5 years ago by
dsull
★ 7.8k • written 4.5 years ago by
dk0319
▴ 70
1
vote
2
replies
1.8k
views
Basic questions about SPAdes, metaSPAdes
metaspades
4.5 years ago by
yingcraft
• 0
0
votes
3
replies
4.9k
views
Questions on ssGSEA
RNA-seq
gsva
ssGSEA
alignment
updated 4.5 years ago by
Brian Gudenas
▴ 90 • written 4.5 years ago by
emi
▴ 80
0
votes
1
reply
751
views
.bam .sam paired or unique aligment
aligment
sam
bam
updated 2.7 years ago by
Ram
45k • written 4.5 years ago by
Roberto Damian
• 0
6
votes
3
replies
1.6k
views
Tool for Protein Alignment/Superimposition
protein
superimposition
alignment
4.5 years ago by
antoniaa
▴ 30
1
vote
3
replies
1.4k
views
Cannot great a gene by gene matrix in Rstudio
gene
matrix
updated 3.0 years ago by
Ram
45k • written 4.5 years ago by
Bioman
• 0
6
votes
10
replies
2.4k
views
what does very low estimates but a significant P value mean.
coefficients
pvalue
regression
updated 4.4 years ago by
Papyrus
★ 3.1k • written 4.5 years ago by
ritz
▴ 10
1
vote
1
reply
1.5k
views
How can I compare the similarities of two transcriptomes?
transcriptome
similarity
rnaseq
updated 4.5 years ago by
Pratik
★ 1.1k • written 4.5 years ago by
avelarbio46
▴ 30
4
votes
6
replies
8.7k
views
calculate ti/tv ratio in WGS data
sequencing
ti/tv ratio
updated 4.5 years ago by
davidc
• 0 • written 7.6 years ago by
chengyi31000
▴ 10
0
votes
1
reply
909
views
what is the length of sliding window in trimming options how to get it
fastq
fasta
SRA
updated 2.7 years ago by
Ram
45k • written 4.5 years ago by
FadyNabil
▴ 20
1
vote
1
reply
2.6k
views
RNA-seq gene list - HOMER Gene based analysis
RNA-Seq
homer
updated 4.5 years ago by
bkleiboeker
▴ 370 • written 8.4 years ago by
G.Car
▴ 20
3
votes
4
replies
2.0k
views
Duplicate ID error with update-name flag
Chromosome
SNP
position
Plink
unix
rsid
updated 4.5 years ago by
zx8754
12k • written 4.5 years ago by
geno89
▴ 20
0
votes
1
reply
1.2k
views
Generating multiple species consensus alignments for tree topology tests
bcftools
alignment
fasta
iqtree
vcf
updated 4.5 years ago by
Arsenal
▴ 160 • written 4.5 years ago by
mglasena
▴ 40
1
vote
8
replies
2.3k
views
How to map rsIDs to KEGG variant Ids
dbsnp
kegg
rsid
4.5 years ago by
david.f.stein
▴ 10
0
votes
1
reply
1.1k
views
blastn cut off values
blast
updated 4.5 years ago by
Arsenal
▴ 160 • written 4.5 years ago by
Wilber0x
▴ 70
2
votes
1
reply
5.6k
views
vcftools and SnpSift give different values for Ts/Tv ratio
variant
SNP
vcf
transversion
transition
updated 4.1 years ago by
Ram
45k • written 10.8 years ago by
ethan.kaufman
▴ 380
13
votes
6
replies
12k
views
6 follow
convert sam into paf format
genome
alignment
sequencing
assembly
SNP
updated 2.9 years ago by
susan.klein
▴ 30 • written 4.9 years ago by
archanaverma433
▴ 10
0
votes
4
replies
1.5k
views
add text to a path by adding text to it with python (FTP Path NCBI)
python
ncbi
pandas
4.5 years ago by
Debut
▴ 20
1
vote
0
replies
938
views
Job:
Opportunity: Bioinformatics Software Engineer - Bioinformatics Core @ Memorial Sloan Kettering Cancer Center, New York, NY (US)
cancer_biology
Python
R
updated 4.4 years ago by
Ram
45k • written 4.5 years ago by
bic-recruit
▴ 10
0
votes
1
reply
857
views
Differential Expression Analysis Using RPKM
RPKM
RNA-seq
DE
updated 4.5 years ago by
swbarnes2
15k • written 4.5 years ago by
bryan.yankee27
• 0
1
vote
1
reply
1.1k
views
Single cell clusters annotating to same cell-type
Monocle
Single-cell
Seurat
Pseudotime
updated 4.5 years ago by
Pratik
★ 1.1k • written 4.5 years ago by
rykerklie7
▴ 50
0
votes
2
replies
1.3k
views
Exact duplicated reads between independent replicates
ChIP
NGS
low-input
duplicates
Illumina
4.5 years ago by
Miguel
• 0
0
votes
1
reply
2.0k
views
Surat object UMAP - highlight cells based on Citeseq data
Seurat
UMAP
updated 4.5 years ago by
antonioggsousa
3.4k • written 4.5 years ago by
chi.delta
▴ 40
2
votes
1
reply
1.1k
views
Obtaining all independent SNPs
SNPs
permutation
pruning
clumping
PLINK
updated 4.5 years ago by
Sam
★ 4.8k • written 4.5 years ago by
KitScorpion
▴ 10
1
vote
2
replies
1.3k
views
Cytoscape for co-occurence network analysis
Microbiome
16S
analysis
Cytoscape
Network
4.5 years ago by
Bioinfonext
▴ 480
3
votes
2
replies
2.4k
views
Structural variants calling in a population
structural variants
updated 4.5 years ago by
Benbird
• 0 • written 8.5 years ago by
guillaume.rbt
★ 1.0k
5
votes
4
replies
7.7k
views
Merge vcf files of structural variants
structural_variants
vcf
merge
updated 4.5 years ago by
Benbird
• 0 • written 7.3 years ago by
ma17
▴ 20
3
votes
2
replies
4.4k
views
For loop to parallel run commands
Unix
bash
Linux
4.5 years ago by
endretoth
▴ 40
122,198 results • Page
640 of 2444
Recent Votes
Answer: Feature Counts vs Salmon quantification
Comment: Feature Counts vs Salmon quantification
Answer: Can i use orthofinder for small protein datasets and not full proteome?
Comment: Comparison of different RNAseq data sets
Comment: ID unifiying across different datasets
Comment: ID unifiying across different datasets
Comment: snpEff: Unsupported structural variant types
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Comment: ID unifiying across different datasets
by
GenoMax
154k
In this case the entry notes that this is likely the product of a pseudogene: https://www.uniprot.org/uniprotkb/Q5VTE0/entry and existence …
Comment: Comparison of different RNAseq data sets
by
DrSmad
▴ 10
Each lab contributes both control and LPS. Example, for cell line A_lab1 did and analysis on control and LPS-6h. Cell line B_lab2 did contr…
Comment: ID unifiying across different datasets
by
zizigolu
★ 4.4k
sorry, why some gene names are often lacking though the Uniprot ID is still valid (using biomart)?
Comment: snpEff: Unsupported structural variant types
by
shpak.max
▴ 70
Unfortunately, while it ran without a problem initially, when I checked the run screen today, I saw the following error message (and unlike…
Comment: ID unifiying across different datasets
by
GenoMax
154k
You can use the [**ID mapping tool**][1] from UniProt site (third ID did not map from the list above): From To P68104 ENSG0000015…
Answer: The geo samples is not having sentrix id and sentrix position. But this informat
by
yura.grabovska
▴ 890
Crosspost from related question: https://www.biostars.org/p/9616466/#9616534 ``` ##Using R, illuminaio from Bioconductor library(…
Answer: Finding Sentrix ID in HM450K arrays
by
yura.grabovska
▴ 890
``` ##Using R, illuminaio from Bioconductor library(illuminaio) temp.idat <- readIDAT(file = "200379120087_R02C02_Grn.idat") tem…
Comment: Can i use orthofinder for small protein datasets and not full proteome?
by
michael.ante
★ 4.0k
Do you want to compare them by sequence or by function? For the later, you can use e.g. InterProScan, KoFamScan.
Answer: Can i use orthofinder for small protein datasets and not full proteome?
by
dthorbur
★ 3.2k
If you're just using the tool for clustering purposes, I think OrthoFinder might be a little clunky and would recommend using something lik…
Comment: ID unifiying across different datasets
by
zizigolu
★ 4.4k
Thank you; The problem is let's say in the protein ID column I see `Q5VTE0;P68104;Q05639` here I am sure I should get which `ENSG` for eac…
Comment: How to improving 2-Nucleotide RNA-seq Mapping Accuracy
by
2411110159
• 0
Since we do not have real data yet, I tried to simulate this using strand-specific RNA bisulfite-seq reads (C to T). Read1 corresponds to t…
Comment: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
by
2411110159
• 0
Very helpful!
Comment: direct RNA long-reads alignment against reference genome
by
frarodmar17
• 0
Okay, thanks! I removed reads.fa and I used the index created with minimap2 in .mmi format. Is this correct?
Comment: Access to bulk FAST5 datasets
by
matt_arnold_bio
• 0
Just bumping this to see if anyone knows where I can download example **bulk** files (i.e. files containing metadata allowing simulated pla…
Answer: direct RNA long-reads alignment against reference genome
by
GenoMax
154k
> Can I align these reads against a reference genome directly? I Yes you can with the following pre-set as noted in `minimap2` quick guid…
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