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514 results • Page
2 of 11
Sort: Votes
Rank
Views
Votes
Replies
2
votes
1
reply
378
views
In GWAS what is the point of regressing a quantitative phenotype on covariates first and taking the residuals?
gwas
updated 22 days ago by
LChart
1.8k • written 23 days ago by
curious
▴ 720
2
votes
5
replies
669
views
comparative transcriptome - how to normalize and analyze DEGs?
RNA-Seq
rna-seq
R
updated 16 days ago by
Lada
▴ 10 • written 2.5 years ago by
nadal-t
▴ 20
2
votes
3
replies
302
views
SALMON Index build Process Killed!
salmon
index
mapping
10 days ago by
Soumajit
▴ 30
2
votes
3
replies
473
views
samtools mpileup error - 1 samples in 1 input files
samtools
bioinformatics
SAM
BAM
mpileup
updated 2 days ago by
Pierre Lindenbaum
152k • written 13 months ago by
joseph.kelly.94
▴ 10
2
votes
1
reply
2.2k
views
A snp caller from a multiple alignment using python/biopython
alignment
SNP
sequence
updated 29 days ago by
Ram
37k • written 7.7 years ago by
cnyaigoti
• 0
2
votes
4
replies
278
views
Retrieve specific fasta sequences from a group of assemblies
CDS
gene
sequence
5 days ago by
SushiRoll
▴ 100
2
votes
1
reply
281
views
STAR paired end mode question
STAR
updated 22 days ago by
ATpoint
68k • written 22 days ago by
Jjbox
▴ 30
2
votes
1
reply
1.2k
views
pair wise differences of different populations
snp
updated 11 days ago by
Ram
37k • written 7.7 years ago by
drshahzadbhatti
• 0
2
votes
12
replies
4.1k
views
Adding barcodes to forward and reverse reads after sequencing
obitools
barcoding
next-gen-sequencing
updated 1 day ago by
Ram
37k • written 7.7 years ago by
cmogren
▴ 20
1
vote
0
replies
120
views
Meta-analysis of rare variant SAIGE-GENE output for WGS data
meta-analysis
rare
SAIGE
variant
8 days ago by
tacrolimus
▴ 100
1
vote
5
replies
526
views
gene ontology of a certain gene names
R
updated 26 days ago by
barslmn
★ 1.2k • written 4 weeks ago by
Bioinfo
• 0
1
vote
1
reply
167
views
How to set NCBI entrez to pipe or ignore errors?
NCBI
Entrez
updated 8 days ago by
GenoMax
125k • written 8 days ago by
rijan_dhakal
• 0
1
vote
1
reply
235
views
calculating the allele frequency of a gene deletion and duplication
cnv
updated 24 days ago by
German.M.Demidov
★ 2.9k • written 25 days ago by
curious
▴ 720
1
vote
4
replies
3.4k
views
BWA MEM alignment output of splited fastq files differ from the original(unsplit) fastq file
next-gen
alignment
updated 29 days ago by
Ram
37k • written 7.7 years ago by
manojkumar_bhosale
▴ 70
1
vote
1
reply
165
views
tools that align sequences in mouse and human
r
updated 4 days ago by
dthorbur
▴ 260 • written 4 days ago by
Chironex
▴ 40
1
vote
1
reply
455
views
Downloading the IMGT/V-QUEST software
vquest
software
updated 11 days ago by
H.Hasani
▴ 990 • written 14 months ago by
rubic
▴ 260
1
vote
1
reply
272
views
How do I subset a dataframe based on several other dataframes using R?
R
affymetrix
updated 2 days ago by
Ram
37k • written 12 months ago by
melissachua90
▴ 40
1
vote
2
replies
194
views
How to install pandas
ml
python
offtopic
updated 5 days ago by
Ram
37k • written 6 days ago by
Sargun
• 0
1
vote
5
replies
226
views
more than one sample in the same fasta file
mirnaseq
usegalaxy
10 days ago by
demoraesdiogo2017
▴ 80
1
vote
1
reply
353
views
Parse error in Autodock Vina
error
Autodock
docking
updated 28 days ago by
mohammadhassanj
▴ 230 • written 28 days ago by
bhavya2269
• 0
1
vote
2
replies
2.5k
views
Why it is important to remove duplicate sequences before a ML tree construction?
viral evolution analysis
Tree construction
gene
updated 15 days ago by
Greg P
▴ 70 • written 6.4 years ago by
armando.torre
▴ 10
1
vote
0
replies
130
views
SNP calling
SNPcalling
16 hours ago by
abozorgmehr1985
▴ 10
1
vote
3
replies
274
views
Calculating PRS in a large cohort
PRS
3 days ago by
haasroni
• 0
1
vote
1
reply
190
views
Aggregate gene expression
AggregateExpression
RNASeq
Seurat
expression
gene
updated 8 days ago by
jv
▴ 780 • written 8 days ago by
Anst
▴ 30
1
vote
1
reply
191
views
How to calculate tumor mutation burden (TMB)?
TMB
Mutations
WES
Sequencing
Mutationrate
updated 7 days ago by
Fabio Marroni
★ 2.9k • written 25 days ago by
tanbiswas6
▴ 10
1
vote
2
replies
295
views
GC content in chip seq data
GC-content
chip-seq
updated 15 days ago by
Ram
37k • written 15 days ago by
Chava
• 0
1
vote
1
reply
178
views
Visualize variants and percentage of variants from one sample of Amplicon Seq data?
Amplicon
PCR
RNAseq
GATK
BWA
updated 2 days ago by
cmdcolin
★ 2.8k • written 4 days ago by
Saran
▴ 20
1
vote
4
replies
3.9k
views
design primer for alternative splicing events
alternative-splicing
primer-design
RNA-Seq
updated 15 days ago by
Ram
37k • written 7.7 years ago by
pengchy
▴ 450
1
vote
13
replies
395
views
RNAseq for DE purpose
RNAseq
updated 2 days ago by
swbarnes2
13k • written 2 days ago by
m.habib
• 0
1
vote
2
replies
250
views
Matching IDs between 3+ files and specifying output using dictionaries in Python
Dictionaries
inforstatements
Matching
loops
Python
9 days ago by
Jennifer
• 0
1
vote
4
replies
3.0k
views
unplaced, unlocalized, ... scaffolds from hg19 to GRCh38
Assembly
updated 3 days ago by
ED
• 0 • written 7.1 years ago by
tabone.olivier
▴ 10
1
vote
3
replies
453
views
Concepts reg Zygosity, copy number variant and variation
number
zygosity
copy
variation
updated 23 days ago by
Mark
★ 1.2k • written 3 months ago by
its.roops
• 0
1
vote
0
replies
153
views
GSEA: different species in gene set and RNA-seq data
RNA-seq
GSEA
14 days ago by
Wang Cong
▴ 10
1
vote
6
replies
716
views
error in pipeline installation dependent on numpy version 1.18.5
cnn
numpy
imaging
python
26 days ago by
Omics data mining
▴ 210
1
vote
9
replies
567
views
Error after installation of AGAT
Perl
AGAT
24 days ago by
L_bioinfo
• 0
1
vote
0
replies
1.8k
views
How to test saturation for codeml in paml?
next-gen
SNP
updated 3 days ago by
Ram
37k • written 7.7 years ago by
xiaofeng.dong12
▴ 20
1
vote
12
replies
3.4k
views
Can anyone explain the weird Insert Size HIstogram
RNA-Seq
alignment
sequencing
updated 29 days ago by
ATpoint
68k • written 5.4 years ago by
SMILE
▴ 170
1
vote
1
reply
119
views
bwa mem duration?
performance
mapping
bwa
updated 1 day ago by
ATpoint
68k • written 1 day ago by
lacb
▴ 30
1
vote
1
reply
1.0k
views
How to interpret highly variable genes plot in Scanpy?
python
single-cell RNA Seq
updated 6 days ago by
mt_pereira
• 0 • written 23 months ago by
Pratik
▴ 870
1
vote
1
reply
219
views
HISAT2 RUNNING ERROR
HISAT2
updated 22 days ago by
ATpoint
68k • written 22 days ago by
SH
• 0
1
vote
6
replies
2.0k
views
Error using samtools for downloading bam files
bam
samtools
updated 2 days ago by
Ram
37k • written 7.7 years ago by
Maria333
▴ 20
1
vote
3
replies
369
views
PCA projection with --score plink2.sscore output: what are the ALLELE_CT & NAMED_ALLELE_DOSAGE_SUM showing?
pca-projection
allele-dosage
score
plink2
updated 22 days ago by
chrchang523
9.9k • written 25 days ago by
ucbtaep
▴ 20
1
vote
1
reply
316
views
HLA typing with archasHLA - DNA seq?
RNA
DNA
arcasHLA
typing
HLA
updated 19 days ago by
fracarb8
▴ 890 • written 22 days ago by
dps2501
• 0
1
vote
6
replies
1.9k
views
How to increase the speed of miRanda target prediction program?
miranada
mirna
parallel
updated 5 days ago by
kuttibiotech2009
▴ 20 • written 5.2 years ago by
lakhujanivijay
5.7k
1
vote
1
reply
129
views
snakemake Unexpected keyword bam in rule definition
snakemake
updated 2 days ago by
Ram
37k • written 2 days ago by
Aidand
• 0
1
vote
0
replies
2.0k
views
Definition of splicing eQTLs in RNA-Seq and arrays
genome
RNA-Seq
snp
updated 1 day ago by
Ram
37k • written 7.7 years ago by
User 7754
▴ 250
1
vote
1
reply
342
views
Getting a PhD in Bioinformatics only having a BSc in Data Science
software-development
project
updated 2 days ago by
Ram
37k • written 12 months ago by
d
• 0
1
vote
3
replies
223
views
Strand-specific in HT-Seq
HT-Seq
Strand-specific
4 days ago by
ibq.enriquepola
• 0
1
vote
8
replies
597
views
Retrieve count table from bam file using genomic coordinates
Sequence
Htseq-count
feature
analysis
counts
updated 25 days ago by
Shred
▴ 990 • written 26 days ago by
L_bioinfo
• 0
1
vote
2
replies
249
views
Get all isoforms and proteins that correspond to list of Trinity gene IDs
fasta
grep
python
isoforms
12 days ago by
cdsparks
• 0
514 results • Page
2 of 11
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Deseq2 with one factor and multiple levels
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1000 genomes project reference panel - GRCh38
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Recent Replies
Comment: PLINK2 selecting variants based on INFO score
by
chrchang523
9.9k
If you aren't willing to provide more precise information than this, sufficient for a reader to reproduce what you're seeing, I will delete…
Answer: Error while trying to install salmon
by
Chris
▴ 10
Donwloading the package from conda (https://anaconda.org/conda-forge/boost/files?version=1.60.0) worked for me wget https://anaconda.org/…
Answer: finding error to run edgeR, error in ploting MDS and after that in model matrix
by
Gordon Smyth
★ 5.4k
First issue is that GEO series matrix files can't be read using `read.delim`. Second issue is the data are from Agilent microarrays and …
Comment: PLINK2 selecting variants based on INFO score
by
m.c.roozen
• 0
I have tried that (the .pvar file contains the "1:10586" form as ID which I mentioned above) which leads to the same output as above, 0 var…
Answer: samtools markdup in Rsamtools
by
joe
▴ 350
You can run any system command from inside R using `system()`. This works well if there is a single command without many dependencies. For …
Comment: samtools markdup in Rsamtools
by
Pierre Lindenbaum
152k
> But other solutions are also fine: bash, nextflow, snakemake
Answer: samtools markdup in Rsamtools
by
ATpoint
68k
My honest opinion: Do processing of sequencing data on the standard command line with samtools. There is no need for the added complexity t…
Comment: To batch correct or analyse separately?
by
predeus
★ 1.8k
Another great and up-to-date resource is this: https://www.sc-best-practices.org/preamble.html
Comment: PLINK2 selecting variants based on INFO score
by
chrchang523
9.9k
The --exclude file must use the same variant IDs as your .pvar file. You should elaborate on what seemed to go wrong when you tried to arr…
Comment: phylogeny
by
炫
• 0
Hello, my problem is the same as yours, did you finally solve this problem?
Comment: phylogeny
by
炫
• 0
您好,我的问题和您的一模一样,请问您这个问题最终解决了吗
Comment: Issue with hmmcalibrate during tutorial.
by
apcreyes29
• 0
If that's the case then I'll just proceed then. Thank you!
Answer: To batch correct or analyse separately?
by
ATpoint
68k
Instead of writing that all down I recommend to read the relevant part of the Bioconductor scRNA-seq book (OSCA) which covers the "how's" a…
Answer: Issue with hmmcalibrate during tutorial.
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Pretty sure that `hmmcalibrate` does not exist in HMMer version 3+ as the models are internally calibrated. I think you are using a manual …
Comment: High downstream gene expression
by
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▴ 10
Thank you for your reply. Your answer has helped me. I am a novice in scientific research, and the reading of literature is really poor. …
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