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121,194 results • Page
8 of 2424
Sort: Rank
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Views
Votes
Replies
0
votes
0
replies
182
views
Significant SNPs with the same effect in FarmCPU
effect-size
gwas
FarmCPU
likage-disequilibrium
6 weeks ago by
AndrMod
• 0
6
votes
11
replies
1.0k
views
Larger genome size than expected-please help
genome
nanopore
size
minimap2
6 weeks ago by
alexandrakortsi
• 0
0
votes
0
replies
237
views
Job:
Postdoc ML/AI in Genomics & Bioinformatics at Duke University
Postodoc
Genomics
AI
6 weeks ago by
alwayshope
▴ 40
0
votes
1
reply
271
views
analyze gene expression of 3 genes in RNA-Seq data
R
RNA-Seq
updated 6 weeks ago by
ATpoint
88k • written 6 weeks ago by
pinheirofabiano
▴ 110
1
vote
1
reply
488
views
methRead takes too long
MethylKit
updated 6 weeks ago by
Alexander Blume
▴ 10 • written 9 months ago by
CTLong
▴ 140
0
votes
0
replies
189
views
rrvgo::getGoSize error
ReViGO
GO-terms
rrvgo
updated 6 weeks ago by
Ram
45k • written 6 weeks ago by
Ana
▴ 10
0
votes
0
replies
179
views
Genotype Imputation for VCF File via API Using R ?
Genotype-Imputation
VCF
API
6 weeks ago by
Ahmed Jaber
• 0
0
votes
0
replies
186
views
How label Group list after integratin scRNA-seq and scATAC-seq data
ArchR
6 weeks ago by
Bioinformatics_16
• 0
0
votes
1
reply
267
views
Forum:
Questions on what to focus on in the next 3-4 years of my research
Career
offtopic
path
5 weeks ago by
Abiodun
• 0
0
votes
7
replies
695
views
Error in importing data from 10x genomics into RStudio
H5
file
scRNA
RStudio
6 weeks ago by
himanshu0102
• 0
1
vote
2
replies
314
views
WGS for CNV and Aneuploidy analysis
CNV
Aneuploidy
WGS
5 weeks ago by
bioinfo1990
▴ 10
0
votes
0
replies
196
views
News:
Course: Phylogenetic Comparative Methods in R – May 12–16 (Online)
R
Phylogenetic-Comparative-Methods
Ultrametric-Phylogenies
updated 6 weeks ago by
Ram
45k • written 6 weeks ago by
Physalia-courses
★ 2.6k
2
votes
2
replies
370
views
Merge and unique multiple complete sam files from identical fastq files
samtools
aligment
sambamba
WGBS
WGS
6 weeks ago by
JustinZhang
▴ 140
0
votes
1
reply
639
views
Issues with T2T in pigeon prepare from isoseq
long-read
isoseq
rna-seq
updated 6 weeks ago by
Ram
45k • written 8 months ago by
SethJ
• 0
1
vote
1
reply
420
views
How to obtain TPM data after batch effect correction from count data obtained using RSEM
STAR
RNA-seq
Batch
RSEM
effect
updated 6 weeks ago by
Gordon Smyth
★ 8.1k • written 6 weeks ago by
Apprentice
▴ 170
2
votes
1
reply
486
views
Missing short indels from vcf
bcftools
shortindels
mpileup
updated 6 weeks ago by
LauferVA
4.7k • written 6 weeks ago by
kbranger
• 0
1
vote
2
replies
420
views
Choosing the best clustering method for a certain methylation data
DMR
k-means
hierarchical
clustering
methylation
updated 6 weeks ago by
5heikki
11k • written 6 weeks ago by
Sophia
• 0
6
votes
16
replies
1.2k
views
MultiQC_report
adapter
Quality-control
fastqc
multiqc
5 weeks ago by
AIMAR
▴ 10
4
votes
3
replies
492
views
Forum:
How to get into research for an absolute beginners
research
updated 6 weeks ago by
Yugan Gogul Muthukumar
▴ 10 • written 6 weeks ago by
jpeduprep
• 0
0
votes
0
replies
249
views
News:
Online course — Comparative Genomics — 7–11 April
SNVs
ComparativeGenomics
SVs
GenomeAnnotation
6 weeks ago by
Physalia-courses
★ 2.6k
0
votes
2
replies
377
views
how to do a corellation analysis of multiple CRISPR data sets
crispr-screen
batch-effect
correlation
updated 6 weeks ago by
Ram
45k • written 6 weeks ago by
Assa Yeroslaviz
★ 1.9k
8
votes
5
replies
735
views
Alternatives to UCSC genome browser for obtaining gene coordinates
browser
ucsc
5 weeks ago by
shpak.max
▴ 60
1
vote
12
replies
987
views
Tool:
Introducing Grantease: Go From RFA to First Draft Grant Proposal in 15 Minutes
ai
biology
grants
nih
litreview
updated 6 weeks ago by
jared.andrews07
★ 18k • written 6 weeks ago by
Will
• 0
0
votes
0
replies
307
views
Job:
Postdoctoral Position in Computational Protein Design and Molecular Modelling
protein-design
molecular-modeling
postdoc
updated 6 weeks ago by
Ram
45k • written 6 weeks ago by
Sophie
• 0
0
votes
1
reply
317
views
How to put distinct colors to connection bridges in the Sankey plot ?
R
Python
Sankey
updated 6 weeks ago by
zx8754
12k • written 6 weeks ago by
ohtang7
▴ 40
1
vote
1
reply
336
views
PCA comparison of cell line vs tumors
RNAseq
Sequencing
PCA
Normalization
updated 6 weeks ago by
ATpoint
88k • written 6 weeks ago by
karlensberg
• 0
2
votes
9
replies
810
views
Find the reads which correspond to DP of vcf
bam
variant
vcf
sam2tsv
updated 6 weeks ago by
Pierre Lindenbaum
166k • written 6 weeks ago by
totoroGirl
• 0
1
vote
1
reply
347
views
cibersortx error - $ operator is invalid for atomic vectors
cibersortx
6 weeks ago by
Franck
• 0
0
votes
0
replies
242
views
Need help defining a threshold
DAVID
Genes
GO
6 weeks ago by
Ana
▴ 10
5
votes
4
replies
509
views
PCA plots in ATAC-seq replicates: Is it okay to use vst transformed data for visualization?
ATAC-seq
diffbind
updated 6 weeks ago by
ATpoint
88k • written 6 weeks ago by
maplewj
▴ 20
0
votes
1
reply
512
views
Question about `vg construct`
vg
updated 6 weeks ago by
Jouni Sirén
▴ 670 • written 7 weeks ago by
zhengluo
• 0
0
votes
0
replies
240
views
How can I use mcmcglmm to calculate whether two traits are correlated?
glmm
statistics
evolution
6 weeks ago by
雨
▴ 20
0
votes
3
replies
1.2k
views
DiffBind normalization error: invalid argument type (list) - cannot make it work, everything seems correct
normalization
deseq2
chipseq
diffbind
6 weeks ago by
buffealo
▴ 130
1
vote
8
replies
1.9k
views
6 follow
FastQC on nanopore data: high proportion of polyA and polyG. Why ?
fastQC
polyG
ONT
nanopore
polyA
updated 6 weeks ago by
lieven.sterck
15k • written 14 months ago by
Matt
• 0
82
votes
32
replies
32k
views
18 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 6 weeks ago by
Paulo
▴ 10 • written 11.3 years ago by
Istvan Albert
102k
1
vote
4
replies
565
views
News:
Wolfram tech for bio data analysis
plots
statistics
databases
ai
6 weeks ago by
dk7258859
• 0
1
vote
2
replies
436
views
MULTIQC for miRNAseq data
multiqc
4 weeks ago by
Alana Conceição Maia Lessa
• 0
0
votes
1
reply
423
views
How to improve the mapping rate of vg giraffe
vg
updated 6 weeks ago by
colindaven
7.4k • written 6 weeks ago by
gulin
• 0
0
votes
6
replies
681
views
miRNA-seq normalization
miRDeep2
normalization
RNA-seq
miRNA-seq
miRNA
6 weeks ago by
paulanavarrete116
• 0
2
votes
2
replies
496
views
Issues with vg surject into paths
vg
updated 6 weeks ago by
GenoMax
151k • written 6 weeks ago by
Rugare
• 0
8
votes
12
replies
912
views
Batch correction RNA-seq analysis
rna-seq
ComBat-seq
batch
correction
updated 6 weeks ago by
LauferVA
4.7k • written 6 weeks ago by
ka132
▴ 10
0
votes
2
replies
427
views
DEG analysys using pseudobulk from single cell RNA-seq
DEG
scRNA-seq
6 weeks ago by
Diego
▴ 110
1
vote
1
reply
318
views
Microarray platform probrID to Circ-ID problem
CircRNA
microarray
updated 6 weeks ago by
GenoMax
151k • written 6 weeks ago by
ParastooA
▴ 20
0
votes
4
replies
462
views
Checking sex of a sample with sequencing data
ATAC-seq
6 weeks ago by
xqyn
▴ 30
2
votes
5
replies
671
views
Depth in Cram file does not match depth in VCF file
IGV
of
Depth
SNV
coverage
updated 6 weeks ago by
Istvan Albert
102k • written 7 weeks ago by
shu8
• 0
1
vote
1
reply
345
views
Tools for clustering genes rather than samples for bulk RNA-seq
time
Bulk
RNA-seq
course
clustering
updated 6 weeks ago by
i.sudbery
21k • written 6 weeks ago by
ATS
• 0
2
votes
2
replies
496
views
what database should I use for de novo genome in AUGUSTUS
genome
AUGUSTUS
galaxy
annotation
updated 6 weeks ago by
lieven.sterck
15k • written 7 weeks ago by
Jl
• 0
1
vote
8
replies
698
views
Is there a tool to obtain GO terms for thousands of genes at once?
permutations
Genes
updated 24 days ago by
GenoMax
151k • written 6 weeks ago by
Ana
▴ 10
0
votes
1
reply
301
views
cant make the correct matrix
logfc
csv
updated 6 weeks ago by
lieven.sterck
15k • written 6 weeks ago by
Naila
• 0
1
vote
4
replies
486
views
FIxing Gene Models in Funannotate
genomics
funannotate
fungus
annotation
6 weeks ago by
SomeOne
▴ 170
121,194 results • Page
8 of 2424
Recent Votes
Comment: How important are allele fractions when calling variants?
Answer: DESeq2 outliers-should I be concerned?
A: fasta to fastq without quality scores
C: fasta to fastq without quality scores
Answer: Cross-species differential gene expression, finding orthologs
C: FRIP score ATAC-seq
Answer: Trimmomatic command
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Recent Replies
Comment: How common is it to split fastq files prior to bwa mem to increase parallelizati
by
dsull
★ 7.5k
Btw, for splitting, in my hands, piping `unpigz` into the unix `split` command seemed to work faster than `seqkit`.
Answer: Download GenomicSEM reference file
by
zhangmyharper
• 0
Sorry for that,I have found it.
Answer: How common is it to split fastq files prior to bwa mem to increase parallelizati
by
dsull
★ 7.5k
Splitting is a good strategy for speeding up processing. I use it all the time in my Snakemake workflows. Processing multiple files in para…
Comment: DESeq2 outliers-should I be concerned?
by
bioinfo
▴ 150
Thank you so much for the explanation!
Comment: How common is it to split fastq files prior to bwa mem to increase parallelizati
by
ATpoint
88k
4GB is in no way enough. The sort alone uses 768MB RAM per thread, so 8*768 already exceeds the memory. bwa with that many threads will use…
Comment: How common is it to split fastq files prior to bwa mem to increase parallelizati
by
curious
▴ 860
This run is running on a node with 60 cores but I only requested 4GB of RAM. Seem like it is only using 2 CPUs to near 100% if I open htop.…
Comment: How common is it to split fastq files prior to bwa mem to increase parallelizati
by
ATpoint
88k
What is your hardware and command line? Two days sounds excessive, unless you are limited by RAM and cores, and that then would make it que…
Comment: Difference in mapping rate when aligned with mapper.pl of miReep2 and bowtie1
by
LINHUI
• 0
Thanks! It worked for me
Comment: Cross-species differential gene expression, finding orthologs
by
fe94
▴ 10
I'm doing a genome-guided assembly (using publicly available genomes info) of the transcripts, we generated RNAseq data for all the species…
Comment: Cross-species differential gene expression, finding orthologs
by
GenoMax
151k
> I'm using genome and gtf info that are publicly available to map and assemble the transcripts for all 3 species. Are you assembling the …
Answer: Longest Protein per Gene from gpff file
by
lieven.sterck
15k
Have a look ar [AGAT][1] , with special focus on the `agat_sp_keep_longest_isoform.pl` subcommand. You might first need to convert the gen…
Comment: Cross-species differential gene expression, finding orthologs
by
fe94
▴ 10
Thank you for the suggestion!! Yes cross-species DEG analysis, especially for non-model species, seems pretty tricky still.
Comment: Cross-species differential gene expression, finding orthologs
by
fe94
▴ 10
Hi GenoMax, I'm not sure I got your question right. I'm using genome and gtf info that are publicly available to map and assemble the trans…
Comment: PRS result interpretation
by
Sam
★ 4.8k
Currently, we still haven't figure out how to best use PRS on individual level. What are your research question? Why do you need to use a P…
Comment: How important are allele fractions when calling variants?
by
Jeremy Leipzig
23k
The allele fraction is the main thing but only after artefactual alignments have been removed. If the AF is .2 but the other .8 of reads sh…
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