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1,154 results • Page
2 of 24
Sort: Rank
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Votes
Replies
0
votes
1
reply
319
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics
bootstrap
updated 1 day ago by
Klaus S
▴ 150 • written 7 days ago by
Zeng Hao
▴ 40
0
votes
2
replies
319
views
How can I solve this error?
metal
1 day ago by
22211020193
• 0
0
votes
0
replies
139
views
Struggling to lift genome builds
PLINK
liftover
GWAS
updated 1 day ago by
GenoMax
141k • written 1 day ago by
srimmer
• 0
1
vote
2
replies
237
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 1 day ago by
Ram
43k • written 1 day ago by
aniigodwinn
• 0
2
votes
3
replies
369
views
Sheep reference genome remapping coordinates
reference
remap
sheep
coordinates
genome
1 day ago by
valentinatsar
• 0
2
votes
3
replies
253
views
Editing Human Reference Genome by adding a CDS
gff
agat
transcriptome
updated 1 day ago by
Michael
54k • written 2 days ago by
LDT
▴ 330
2
votes
10
replies
609
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 23 hours ago by
GenoMax
141k • written 2 days ago by
me
• 0
2
votes
2
replies
347
views
differential gene expression analysis when not all samples have an untreated counterpart
differential-expression
edgeR
23 hours ago by
nhaus
▴ 300
0
votes
0
replies
271
views
Looking for an explanation as to what the Peak Score is from HOMER, not finding any answers on Biostars yet
Homer
ATAC-seq
2 days ago by
Ronin
• 0
4
votes
2
replies
1.7k
views
How to convert SAM/BAM file to GTF/GFF file?
GTF
SAM
BAM
GFF
minimap2
updated 2 days ago by
Dr.Animo
▴ 130 • written 11 months ago by
BioinfoBee
• 0
2
votes
7
replies
703
views
Removing duplicates
duplicates
ONT
minimap2
updated 16 hours ago by
joe
▴ 510 • written 2 days ago by
quentinperriere
• 0
0
votes
1
reply
167
views
Annotating a dataset with gnomAD v4 using Hail
Python
Sequencing
Hail
Exome
Annotation
updated 2 days ago by
DKA
▴ 40 • written 2 days ago by
james.melhorn
• 0
3
votes
4
replies
357
views
biomaRt error for different R version
biomaRt
R
updated 1 day ago by
GenoMax
141k • written 2 days ago by
manaswwm
▴ 490
0
votes
1
reply
157
views
Freyja plot error
Freyja
updated 2 days ago by
Ram
43k • written 2 days ago by
Adyasha
• 0
1
vote
2
replies
165
views
Interpretation of combined P values - RNA microarray meta analysis
metaanalysis
R
microarray
DExMA
combinedP
2 days ago by
hagl
▴ 10
0
votes
0
replies
124
views
BIOM format can contain tabular data ?
BIOM
phyloseq
biomformat
R
2 days ago by
chemokine-1
▴ 10
0
votes
4
replies
430
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
1 day ago by
feather-W
• 0
0
votes
0
replies
186
views
Job:
Consultant to update a Snakemake workflow with the new Kubernetes executor plugin for Snakemake 8
Kubernetes
DevOps
executor
AWS
Snakemake
updated 2 days ago by
Michael
54k • written 2 days ago by
jonrkarr
▴ 100
0
votes
2
replies
184
views
Bedmethyl file format
bedmethyl
methylation
updated 2 days ago by
GenoMax
141k • written 2 days ago by
njornet
▴ 20
0
votes
0
replies
142
views
sequence table for DADA2 chimera filtering
OTU
sequencetable
DADA2
2 days ago by
Ali
• 0
2
votes
4
replies
274
views
SnpEff annotates coding duplication as intronic?
snpeff
2 days ago by
kirill.zaslavsky
• 0
0
votes
2
replies
211
views
Calculating percentage of cells proliferating in single cell rna seq data
statistics
scRNA-seq
proliferation
2 days ago by
mropri
▴ 150
5
votes
4
replies
2.8k
views
genefu for PAM50 prediction
RNA-Seq
breast cancer
subtyping
updated 2 days ago by
hamarillo
▴ 70 • written 5.6 years ago by
silviajserrano
▴ 50
3
votes
10
replies
574
views
Piping samtools to R
R
NGS
bash
samtools
2 days ago by
joe
▴ 510
2
votes
2
replies
208
views
How to filter columns in a raw sparse matrix in R
matrix
R
updated 2 days ago by
bk11
★ 2.3k • written 2 days ago by
bgbs
• 0
3
votes
7
replies
379
views
Integration of transcriptomics and proteomics: difficult matching names
rna-seq
tmt
nomenclature
proteomics
2 days ago by
ntsopoul
▴ 60
0
votes
0
replies
125
views
Input into WGCNA and Error on constructNetworks on RNA-Seq data - unique rownames
rownames
RNA-Seq
WGCNA
unique
2 days ago by
shasabhi1
• 0
0
votes
0
replies
120
views
How to summarize dbCAN3 results
dbCAN
CAZy
CAZyme
dbCAN3
dbCAN2
2 days ago by
Nishat
• 0
3
votes
3
replies
377
views
trouble using sequenceTubeMap in chromium installed on WSL
vg
2 days ago by
ayushm64
• 0
0
votes
0
replies
132
views
what exactly is a k-mer table (remora)?
remora
basecall
2 days ago by
anne
• 0
3
votes
6
replies
10k
views
List of species in RepeatMasker Tool (species parameter)
RepeatMasker
Masking
updated 2 days ago by
Bioinfotec
▴ 10 • written 7.5 years ago by
nut_B
▴ 10
1
vote
6
replies
344
views
Rename multiple fastq.gz files
fastq
next-gen
updated 2 days ago by
shenwei356
8.4k • written 2 days ago by
Jérémie
• 0
1
vote
1
reply
155
views
Help/Direction Needed for Data Analysis of RNA
Sequencing
RNA-seq
DNA-Seq
updated 2 days ago by
dsull
★ 5.8k • written 2 days ago by
niruf
• 0
0
votes
0
replies
155
views
Job:
Ensembl Outreach Project Leader
ebi
embl
genomics
ensembl
3 days ago by
Ben_Ensembl
★ 2.4k
2
votes
3
replies
242
views
Bwa sampe - BGI
Bwa-sampe
BGI
updated 3 days ago by
GenoMax
141k • written 3 days ago by
lorena9132
• 0
0
votes
0
replies
155
views
News:
Final Call - Bioinformatics Pipeline Development with Nextflow (May 27-29, 2024)
workshop
RNA-seq
nextflow
DNA-seq
updated 2 days ago by
Ram
43k • written 3 days ago by
David Langenberger
11k
0
votes
0
replies
127
views
GWAS Phenotypes
GWAS
3 days ago by
solomoncharles77
▴ 90
4
votes
2
replies
232
views
Forum:
Bioinformatics: Where do I start
Sequencing
updated 2 days ago by
Ram
43k • written 3 days ago by
Adi
▴ 10
0
votes
2
replies
285
views
GSEA analysis in R
GSEA
R
Arabidopsis
1 day ago by
Sudip
• 0
1
vote
2
replies
235
views
Visualization of PROKKA Annotation Result?
PROKKA
Annotation
updated 3 days ago by
Joe
21k • written 4 days ago by
ferdinand
▴ 10
0
votes
2
replies
343
views
Which experiments generate Position Frequency Matrix?
Position-Frequency-Matrix
1 day ago by
arriyaz.nstu
▴ 30
2
votes
2
replies
358
views
I am new to single cell analysis. Can RNA velocity (spliced/unspliced) be calculated solely from the raw file (count matrix) provided in the Suppleme…
GEO
velocity
count-matrix
updated 2 days ago by
Ram
43k • written 3 days ago by
Spring
• 0
0
votes
0
replies
107
views
Add geno header to VariantAnnotation objects
nichenet
scRNA-seq
3 days ago by
QX
• 0
5
votes
4
replies
253
views
I'm new to cell ranger. Can single cells prepared with a protocol other than the 10x genomics protocol not be processed with cell ranger?
cellranger
scRNA-seq
10x
3 days ago by
Spring
• 0
2
votes
5
replies
350
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats
hg002
bed
homopolymer-regions
2 days ago by
Bikram Kumar
• 0
1
vote
1
reply
275
views
WGCNA network from Adjacency or TOM matrix
WGCNA
network
updated 3 days ago by
andres.firrincieli
3.6k • written 7 days ago by
Milly
• 0
0
votes
1
reply
197
views
Error in edgeR/Deseq2 Analysis
r
edger
updated 3 days ago by
ATpoint
81k • written 3 days ago by
Ravita
• 0
0
votes
2
replies
203
views
Getting marker genes for cell types
clustering
marker-genes
umap
3 days ago by
orzrzlyo
▴ 20
0
votes
1
reply
197
views
gene body coverage with RSeqQC
rna-seq
qc
updated 3 days ago by
BioinfGuru
★ 1.7k • written 3 days ago by
wiscoyogi
▴ 40
0
votes
2
replies
227
views
Statistical Advice Needed for RNAseq Data Analysis
Statistical-Significance
Genomics
RNA-seq
Data-Analysis
updated 2 days ago by
Ram
43k • written 3 days ago by
David
• 0
1,154 results • Page
2 of 24
Recent Votes
Answer: Problem with Sniffles pipeline and SV calling help
Illumina reads preprocessing best practice for snp calling applications
Comment: Illumina reads preprocessing best practice for snp calling applications
Installing/switching between versions of R/Rstudio/Bioconductor
How To Generate Phylogeny Tree, Based On Snps?
How To Construct Phylogenetic Tree Using Snps
Basic normalization, batch correction and visualization of RNA-seq data
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DanielEB_fisk
▴ 20
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Pierre Lindenbaum
161k
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19k
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Recent Replies
Comment: Illumina reads preprocessing best practice for snp calling applications
by
Enrique
• 0
Hi! I'm still interested in the step that you use for the SNP calling. Did you use `trimmomatic` or another tool for trimming before mappin…
Comment: Could you please assist in identifying this cluster?
by
ATpoint
81k
The information do not suffice. Please show plots and identified marker genes. Also, make sure it is not a trash cluster with low number of…
Comment: Free/open source 23andme-like analysis
by
joe
▴ 510
Thank you, I added 'accurate' now ;) I'm surprised to find out that there isn't some tool like multiqc that just summarizes all this infor…
Comment: Memory usage of picard Samsort
by
ATpoint
81k
Guys, just use `samtools sort` which won't get you into trouble with any of that.
Comment: Ciriquant not configuring hisat2 indexed files
by
Carlo Yague
8.6k
I don't know for sure, but I think that decreasing the amount of threads (1 or 2 instead of 4) will decrease the memory requirements of the…
Answer: Memory usage of picard Samsort
by
tamas.malkocs
• 0
For me, setting `TMP_DIR` (`--TMP_DIR /home/tmp`) didn't work in picard 2.21.1. What solved the issue was setting the environmental variabl…
Answer: Plink merge errors.
by
Dinmukhamed
• 0
I found answer https://www.biostars.org/p/101191/.
Comment: Ciriquant not configuring hisat2 indexed files
by
Atul K.
• 0
it worked. Thank you. Now my terminal is crashing, seems 16gb of RAM and 4 cores isn't enough. Can you suggest something?
Comment: Adding CB tag to bam file
by
Maria
• 0
I checked Picard ```AddOrReplaceReadsGroups``` and ```AddOATag```. Is that what you're referring to?
Comment: Free/open source 23andme-like analysis
by
Michael
54k
Noted that 'accurate' wasn't among your criteria ;) Anyway, most variant callers are free open-source software. However, for ancestry ana…
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi
by
Pierre Lindenbaum
161k
> server so I cannot use Blat for this purpose. blat is avilable as a standane tool: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86…
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi
by
b.contreras.moreira
▴ 160
My favourite for this task would be [GMAP]( http://research-pub.gene.com/gmap ), which can produce GFF format with option `-f 2`. It is…
Answer: Prediction of Ribosomal RNA Genes Using RNAmmer Software
by
colindaven
6.3k
Another alternative is the truly free implementation barrnap https://github.com/tseemann/barrnap. This is also installable via conda so qui…
Comment: Filtration Of Reads With Length Lower Than 30 From Bam
by
Hagen
▴ 10
thanks! This saved me quite some time, I was about to write code to calculate the aligned length from the CIGAR. But this can be done with …
Comment: Per base sequence content failed miserably
by
Kai Xin
• 0
will look into that. Thank you very much
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