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120,932 results • Page
1 of 2419
Sort: Rank
Rank
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Votes
Replies
0
votes
0
replies
18
views
GTDB-tk classify_wf
GTDB-tk
classification
taxonomic
1 hour ago by
pranjalarun10
• 0
0
votes
1
reply
391
views
Help finding proteases that most likely cleaved a peptide from a full-length protein
R
peptides
proteasix
updated 2 hours ago by
Fatemeh
▴ 40 • written 18 months ago by
georgiamorgannn
• 0
0
votes
0
replies
30
views
Batch effect
BatchEffect
RNAseq
2 hours ago by
Fatemeh
▴ 40
836
votes
169
replies
172k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 6 months ago by
Biostar
3.4k • written 8.3 years ago by
Istvan Albert
102k
0
votes
0
replies
27
views
protease candidates for my protein of interest
cleaving-site
proteases
protein
2 hours ago by
Fatemeh
▴ 40
0
votes
5
replies
102
views
Which tools use or rely on the XA tag in SAM/BAM/CRAM files?
cram
XA
compress
updated 1 hour ago by
GenoMax
150k • written 4 hours ago by
Maarten
• 0
0
votes
1
reply
840
views
ADMIXTOOLS: qp3pop fatal error (probably missing pop)
qp3pop
f3test
admixtools
updated 4 hours ago by
Duy
• 0 • written 2.8 years ago by
francesco.fontani2
• 0
0
votes
1
reply
100
views
Annotate GFA with coverage depth
vg
updated 10 hours ago by
Jordan M Eizenga
▴ 690 • written 22 hours ago by
elcortegano
▴ 210
0
votes
1
reply
231
views
Query coverage high, E-value low, and identity low - Blastp results interpretation and article recommended?
blastp
protein
sequence
analysis
updated 10 hours ago by
Mensur Dlakic
★ 29k • written 15 hours ago by
Luana JBC
• 0
0
votes
0
replies
52
views
Need Help Regarding Back-Splicing Junction Coordinates in CIRI2 Output
circRNA
CIRI2
updated 12 hours ago by
GenoMax
150k • written 12 hours ago by
Faraz
• 0
0
votes
2
replies
190
views
Methods for directional pathway analysis of DEGs?
Pathway
ORA
GSEA
analysis
Limma
updated 13 hours ago by
Gordon Smyth
★ 7.9k • written 1 day ago by
Steven
• 0
1
vote
0
replies
76
views
Short reads to identify stuctural variants
SV
long-read
short-read
updated 21 hours ago by
Ram
45k • written 21 hours ago by
priya.bmg
▴ 70
0
votes
0
replies
157
views
Best approach for SNP calling in tumor single-cell multiome data (scRNA-seq + scATAC-seq) for CNV analysis
variant
SNP
single-cell
14 hours ago by
nilaylale88
• 0
0
votes
0
replies
98
views
News:
News:Workshop:Virtual Genome Assembly, April 15-17
virtual-workshop
Genome-Assembly
UConn
updated 21 hours ago by
Ram
45k • written 22 hours ago by
zsc25001
• 0
0
votes
3
replies
166
views
C.reinhardtii single-cell Seurat object - gene names instead of loci
loci
Chlamydomonas
single-cell
updated 22 hours ago by
GenoMax
150k • written 23 hours ago by
Ana
• 0
0
votes
3
replies
130
views
Snakemake Global Environment Container
Snakemake
Conda
Singularity
updated 4 hours ago by
DBScan
▴ 470 • written 1 day ago by
meetmet
• 0
0
votes
0
replies
97
views
GTF repeatmasker annotation file
repeatmasker
GTF
1 day ago by
frarodmar17
• 0
0
votes
2
replies
1.3k
views
Searching for online tools to prepare mitochondrial codon usage
genome
updated 1 day ago by
aboozar.soorni
▴ 30 • written 4.6 years ago by
puipui
• 0
1
vote
1
reply
110
views
Getting sequences fragments using pysam
sequencing
pysam
reads
wgs
updated 1 day ago by
i.sudbery
21k • written 1 day ago by
Juls
• 0
6
votes
9
replies
2.9k
views
Does EnhancedVolcano() supports crosstalk()?
EnhancedVolcano
crosstalk
R
ggplot
updated 1 day ago by
GenoMax
150k • written 5.2 years ago by
IrK
▴ 100
0
votes
1
reply
103
views
How to select GEO datasets for differential expression analysis using GEO2R
GEO
DEGs
GEO2R
updated 1 day ago by
ATpoint
87k • written 1 day ago by
dreamer247
• 0
0
votes
0
replies
110
views
Blog:
Unlocking the Cellular Universe: The Importance of Single-Cell Sequencing in Animal and Plant Research
Single-cell
1 day ago by
Novogene
▴ 500
0
votes
4
replies
691
views
PopGenome lost individual information
PopGenome
updated 1 day ago by
Arup Ghosh
3.3k • written 12 months ago by
Yixuan
• 0
1
vote
1
reply
148
views
Question About Handling Technical Replicates in ATAC-seq
technical-replicate
atacseq
updated 1 day ago by
rfran010
★ 1.4k • written 1 day ago by
LuciaNhu
▴ 10
12
votes
16
replies
18k
views
8 follow
How to convert vcf to 23andme format
genome
sequencing
SNP
updated 1 day ago by
ngelbal
• 0 • written 7.5 years ago by
alec_djinn
▴ 390
0
votes
7
replies
281
views
Poor alignment rates using Bowtie
aligment
bowtie2
bowtie
miRNAs
updated 12 minutes ago by
Istvan Albert
102k • written 1 day ago by
omicon
▴ 40
1
vote
5
replies
215
views
Polishing raw nanopore reads with Pacbio
polishing
assembly
17 hours ago by
samuel.a.odonnell
▴ 590
2
votes
4
replies
438
views
bbduk.sh trimming to BAM output file
bbduk.sh
updated 1 day ago by
Brian Bushnell
20k • written 7 days ago by
bge
• 0
0
votes
3
replies
223
views
Identifying domain of long-read assembled contig
longread
taxonomy
identification
contig
updated 1 day ago by
Mensur Dlakic
★ 29k • written 2 days ago by
Gio
• 0
0
votes
6
replies
245
views
Discrepancy between positions on IGV and NCBI's PrimerBLAST
igv
primer
blast
1 hour ago by
Rozita
▴ 40
0
votes
1
reply
148
views
Why does Radian run so much slower than vanilla R?
R
Python
Radian
VS-Code
updated 20 hours ago by
Istvan Albert
102k • written 1 day ago by
RR
• 0
4
votes
9
replies
371
views
About the Tool FASTP
Quality-control
reads
fastp
updated 1 day ago by
shelkmike
★ 1.5k • written 2 days ago by
AIMAR
• 0
0
votes
0
replies
93
views
Significant SNPs with the same effect in FarmCPU
effect-size
gwas
FarmCPU
likage-disequilibrium
2 days ago by
AndrMod
• 0
6
votes
11
replies
753
views
Larger genome size than expected-please help
genome
nanopore
size
minimap2
2 days ago by
alexandrakortsi
• 0
0
votes
0
replies
124
views
Job:
Postdoc ML/AI in Genomics & Bioinformatics at Duke University
Postodoc
Genomics
AI
2 days ago by
alwayshope
▴ 40
0
votes
1
reply
160
views
analyze gene expression of 3 genes in RNA-Seq data
R
RNA-Seq
updated 1 day ago by
ATpoint
87k • written 2 days ago by
pinheirofabiano
▴ 100
1
vote
1
reply
382
views
methRead takes too long
MethylKit
updated 2 days ago by
Alexander Blume
▴ 10 • written 7 months ago by
CTLong
▴ 140
0
votes
0
replies
110
views
rrvgo::getGoSize error
ReViGO
GO-terms
rrvgo
updated 1 day ago by
Ram
45k • written 2 days ago by
Ana
• 0
0
votes
0
replies
107
views
Genotype Imputation for VCF File via API Using R ?
Genotype-Imputation
VCF
API
2 days ago by
Ahmed Jaber
• 0
0
votes
0
replies
125
views
How label Group list after integratin scRNA-seq and scATAC-seq data
ArchR
2 days ago by
Bioinformatics_16
• 0
0
votes
1
reply
188
views
Forum:
Questions on what to focus on in the next 3-4 years of my research
Career
offtopic
path
1 day ago by
Abiodun
• 0
0
votes
7
replies
455
views
Error in importing data from 10x genomics into RStudio
H5
file
scRNA
RStudio
1 day ago by
himanshu0102
• 0
1
vote
2
replies
233
views
WGS for CNV and Aneuploidy analysis
CNV
Aneuploidy
WGS
1 day ago by
bioinfo1990
▴ 10
0
votes
0
replies
140
views
News:
Course: Phylogenetic Comparative Methods in R – May 12–16 (Online)
R
Phylogenetic-Comparative-Methods
Ultrametric-Phylogenies
updated 1 day ago by
Ram
45k • written 3 days ago by
Physalia-courses
★ 2.6k
2
votes
2
replies
277
views
Merge and unique multiple complete sam files from identical fastq files
samtools
aligment
sambamba
WGBS
WGS
2 days ago by
JustinZhang
▴ 120
0
votes
1
reply
544
views
Issues with T2T in pigeon prepare from isoseq
long-read
isoseq
rna-seq
updated 1 day ago by
Ram
45k • written 6 months ago by
SethJ
• 0
1
vote
1
reply
337
views
How to obtain TPM data after batch effect correction from count data obtained using RSEM
STAR
RNA-seq
Batch
RSEM
effect
updated 4 days ago by
Gordon Smyth
★ 7.9k • written 4 days ago by
Apprentice
▴ 170
1
vote
1
reply
382
views
Missing short indels from vcf
bcftools
shortindels
mpileup
updated 4 days ago by
LauferVA
4.7k • written 7 days ago by
kbranger
• 0
4
votes
6
replies
567
views
Facing issue with output of nextflow pipeline
output
nextflow
fastqc
issue
updated 4 days ago by
mmhryc
• 0 • written 7 days ago by
harsh
▴ 20
1
vote
2
replies
315
views
Choosing the best clustering method for a certain methylation data
DMR
k-means
hierarchical
clustering
methylation
updated 4 days ago by
5heikki
11k • written 5 days ago by
Sophia
• 0
120,932 results • Page
1 of 2419
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Answer: Adding Read Groups To Bam Files
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Answer: salmon with long read
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Snpeff: clarification on gene fusion annotation
Short reads to identify stuctural variants
Answer: Sequence Alignment from Scratch with BWA
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Comment: Poor alignment rates using Bowtie
by
Istvan Albert
102k
Needs a summary :-) and TLDR: It looks like references with U do not work correctly with bowtie 1.
Comment: Which tools use or rely on the XA tag in SAM/BAM/CRAM files?
by
GenoMax
150k
> Keeping this amount of data online in the cloud would cost 16K a year, so there is a bit of money True, but if you expect a number of pe…
Comment: Which tools use or rely on the XA tag in SAM/BAM/CRAM files?
by
Maarten
• 0
> Curious as to how you calculated this? I used [samtools cram-size][1] to calculate this. I already played around with genozip, and it …
Comment: Discrepancy between positions on IGV and NCBI's PrimerBLAST
by
Rozita
▴ 40
Yes, I did. I entered the positions of the primers from PrimerBLAST in a CSV file then converted it to a BED file which opens successfully …
Comment: Which tools use or rely on the XA tag in SAM/BAM/CRAM files?
by
GenoMax
150k
> files contain the optional XA:Z tag, which takes 22% of the total filesize Curious as to how you calculated this? If you are that wor…
Comment: Which tools use or rely on the XA tag in SAM/BAM/CRAM files?
by
Maarten
• 0
Thanks for the answer. I moved in experiments from cram 3.0 to cram 3.1 small,lossy_names=1. However, the compression of this block (gzip) …
Comment: Help finding proteases that most likely cleaved a peptide from a full-length pro
by
Fatemeh
▴ 40
Hi Ram, Did you find any method for that? I am also having the same request.
Comment: Which tools use or rely on the XA tag in SAM/BAM/CRAM files?
by
ATpoint
87k
I can only strongly recommend to not mess with BAM files like this. At worst any downstream tool might simply check for presence of some ta…
Comment: Snakemake Global Environment Container
by
DBScan
▴ 470
You can try to add `software-deployment-method: conda singularity` to you profile, this should work accordin to [https://snakemake.readthed…
Comment: Snakemake Global Environment Container
by
meetmet
• 0
Hello, I run snakemake from the main directory of the workflow: snakemake --profile workflow/profile --configfile .test/config/confi…
Answer: ADMIXTOOLS: qp3pop fatal error (probably missing pop)
by
Duy
• 0
To all the future viewers who might experience this problem, I updated the third column in my .ind file to the corresponding population nam…
Comment: MultiQC_report
by
AIMAR
• 0
Thanks for the reply @ewels Now It becomes clear.
Answer: Annotate GFA with coverage depth
by
Jordan M Eizenga
▴ 690
You can annotate Bandage visualizations using a CSV with a certain structure, so you can process the `vg depth` TSV into Bandage's expected…
Answer: Query coverage high, E-value low, and identity low - Blastp results interpretati
by
Mensur Dlakic
★ 29k
Either you are not clear what homologous sequences mean, or you are using some internal definition that makes sense to you. Let's pick an `…
Answer: Methods for directional pathway analysis of DEGs?
by
Gordon Smyth
★ 7.9k
limma provides a suite of directional pathway analysis functions that are integrated with its DE procedures. They are based on competitive …
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