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117,476 results • Page
1 of 2350
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Votes
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0
votes
0
replies
24
views
Why there are only two .fastq files in scATAC-seq raw data?
scATAC-seq
processing
2 hours ago by
浩然
• 0
1
vote
3
replies
1.4k
views
How to measure pairwise genetic distance in all samples of a VCF file
pop-gen
pairwise-distance
VCF
updated 4 hours ago by
hewm2008
▴ 40 • written 19 months ago by
LDT
▴ 340
0
votes
2
replies
116
views
Removing batch effect in time-series data
batch
effect
8 hours ago by
Álvaro
• 0
0
votes
5
replies
172
views
How to download a file from zenodo link without leaving terminal?
axel
downloading_file
curl
wget
linux
updated 7 hours ago by
GenoMax
143k • written 11 hours ago by
SlowSD
• 0
0
votes
1
reply
78
views
Interproscan
configuration
install
interproscan
exist
not
updated 12 hours ago by
Dunois
★ 2.5k • written 12 hours ago by
antochirico98
• 0
808
votes
167
replies
146k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 12 days ago by
Biostar
2.9k • written 7.5 years ago by
Istvan Albert
101k
1
vote
8
replies
241
views
BCFtools not calling variant, despite adequate coverage
bcftools
variant
calling
updated 7 hours ago by
GenoMax
143k • written 12 hours ago by
mpiersonsmela
• 0
0
votes
0
replies
52
views
New versions of the same transcripts ID may have different exons coordinates??
RefSeq
12 hours ago by
ManuelDB
▴ 80
0
votes
1
reply
75
views
How can I get the total list of RefSeq transcripts?
RefSeq
updated 12 hours ago by
GenoMax
143k • written 13 hours ago by
ManuelDB
▴ 80
3
votes
12
replies
827
views
7 follow
Failed to download data from EBI BioStudies with ascp/Aspera
aspera
EBI
updated 19 hours ago by
ruiyan_hou
• 0 • written 9 weeks ago by
biock
▴ 70
0
votes
1
reply
107
views
Problem in input data loading in Structure
Structure-Pritchard
updated 10 hours ago by
Mensur Dlakic
★ 27k • written 20 hours ago by
RN
• 0
0
votes
0
replies
75
views
running multiple GEO Dataset projects
GEO
updated 16 hours ago by
Ram
44k • written 1 day ago by
analyst
▴ 50
0
votes
0
replies
85
views
MEME PWM format - what is the meaning of nsites?
motif
sequence
meme-suite
pwm
meme
1 day ago by
mcsimenc
▴ 20
1
vote
2
replies
212
views
Example human WGS fastq data
WGS
updated 1 day ago by
Ming Tommy Tang
★ 4.0k • written 2 days ago by
ramiro.barrantes
• 0
0
votes
2
replies
189
views
Download SRR by parallele and fastq dump with a wired problem
linux
scRNA-seq
parallel
15 hours ago by
diqixiaoyaoer
▴ 20
0
votes
0
replies
84
views
Tutorial:
Seurat Object Explained: Beginner's Guide and Demo
scRNA-seq
Seurat
single-cell
updated 16 hours ago by
Ram
44k • written 1 day ago by
Ming Tommy Tang
★ 4.0k
0
votes
1
reply
152
views
Empty txt file as an output of "seqkit stats" for multiple fastq files
NGS
Linux
updated 1 day ago by
shenwei356
8.5k • written 1 day ago by
Mohamed Samir
▴ 30
0
votes
3
replies
220
views
how linearize nucleotide lines in axt file
axt
updated 16 hours ago by
Ram
44k • written 1 day ago by
resug
▴ 30
0
votes
0
replies
100
views
How to Merge Single Chromosome Genomic Annotations
BRAKER3
genome
annotation
1 day ago by
Kinoppy
• 0
5
votes
6
replies
341
views
Alignment tool for very short reads (25bp)
mapper
aligner
bwa
alignment
bowtie2
updated 1 day ago by
Ming Tommy Tang
★ 4.0k • written 2 days ago by
arriyaz.nstu
▴ 50
0
votes
0
replies
275
views
Job:
PhD-position in bioinformatics / computational biology (75% E13) at Ruhr-University Bochum
NGS
aging
Epigenomics
mole-rat
omics
1 day ago by
Arne.Sahm
• 0
0
votes
0
replies
104
views
What path list should be used to surject GAM to GRCh38/CHM13 reference genome
vg
1 day ago by
Hanc
• 0
1
vote
4
replies
269
views
Help aligning Nanopore Long Read RNA seqs
rna-seq
long-read
minimap2
updated 1 day ago by
rfran010
▴ 960 • written 2 days ago by
sewaw37819
• 0
0
votes
1
reply
165
views
Job:
postdoc/master's position AI ML
python
Neuroscience
machine-learning
updated 16 hours ago by
Ram
44k • written 2 days ago by
sivan.kinreich
• 0
0
votes
1
reply
154
views
Is T2T genome a "alternate assembly"
T2T
grch38
alternate_assembly
ref_genome
updated 15 hours ago by
GenoMax
143k • written 2 days ago by
Daniel
• 0
3
votes
2
replies
240
views
edgeR batch effect model matrix sanity check
R
edgeR
RNA-seq
batch-effect
1 day ago by
kmyers2
▴ 90
0
votes
2
replies
193
views
minimap2 U to T conversion
minimap2
2 days ago by
kewoka9286
• 0
2
votes
9
replies
303
views
BBMap Excess Fold Coverage
bbmap
2 days ago by
shacon
• 0
0
votes
1
reply
155
views
Jellyfish docker image error with bam files
jellyfish
docker
kmers
updated 2 days ago by
bhumm
▴ 160 • written 2 days ago by
enee
▴ 10
3
votes
4
replies
270
views
Overrepresented sequence in reverse read
FastQC
Genomics
Trimmomatic
Sequencing
ATAC
2 days ago by
Jaskaran Singh
• 0
1
vote
1
reply
238
views
What is the difference between the taxonomy classification and binning in metagenomic?
binning
taxonomy
metagenomic
updated 2 days ago by
Ram
44k • written 4 days ago by
QuotoAstro
• 0
0
votes
0
replies
138
views
Testing difference in median of clinical variabls in Rna-seq data
clinical-features
RNA-seq
updated 2 days ago by
Ram
44k • written 2 days ago by
Znow
▴ 10
0
votes
1
reply
182
views
Split the fastqc file base on barcode
fastq
updated 2 days ago by
GenoMax
143k • written 2 days ago by
QX
▴ 20
5
votes
7
replies
306
views
Illumina Raw Data Multiple Read FIles Discussion
novaseqX
pairedend
illumina
fungus
2 days ago by
Umer
▴ 80
4
votes
4
replies
383
views
Intuitive Graphical Interface for Executing nf-core Pipelines
GUI
genomics
ngs
updated 2 days ago by
Ram
44k • written 4 days ago by
Nour-eddine
▴ 30
0
votes
0
replies
142
views
Enriched Bar Chart on Blast2go gives percentage more than 100%
Blast2go
updated 2 days ago by
Ram
44k • written 2 days ago by
Mohamed Abderrahmane
▴ 20
0
votes
0
replies
138
views
Removing inherent biomarker sensor signals from the actual sensor readings
python
data
noise
2 days ago by
bluecipher
• 0
0
votes
2
replies
480
views
How to use topGO tool for enrichment analysis of non-model organisms
topGO
updated 2 days ago by
wdlin
• 0 • written 4 months ago by
otieno43
▴ 30
2
votes
3
replies
317
views
RSEM getting TPM from STAR alignment
TPM
STAR
RNAseq
RSEM
3 days ago by
Emily
▴ 20
0
votes
0
replies
152
views
Help : Run EVE for CAMK2A.
VEP
EVE
3 days ago by
Meto
• 0
2
votes
3
replies
271
views
Is TMM apropriated for Welch test between gender?
welch-test
TMM
updated 2 days ago by
Ram
44k • written 3 days ago by
Znow
▴ 10
0
votes
4
replies
327
views
SPAdes error when trying to specify options for path
spades
updated 3 days ago by
Mensur Dlakic
★ 27k • written 3 days ago by
AINUR FATIN BINTI MAZRI
• 0
0
votes
1
reply
189
views
Poor alignment post-SortMeRNA (rRNA removal)
STAR
rRNA
RNAseq
SortMeRNA
updated 3 days ago by
andres.firrincieli
3.6k • written 3 days ago by
Fossil
▴ 20
0
votes
1
reply
304
views
How to extract gene_counts_length_scaled matrix from either raw count matrix or SE object
recount3
salmon
gtex
tximport
deseq2
updated 3 days ago by
ATpoint
83k • written 3 days ago by
Aditya
• 0
0
votes
2
replies
262
views
how to see Pacbio reads in IGV
pbmm2
pbindex
Pacbio
long-reads
revio
updated 2 days ago by
Pierre Lindenbaum
162k • written 3 days ago by
María José
• 0
1
vote
1
reply
356
views
TensorQTL Mapping - permutation p values for all associations
permutation
TensorQTL
3 days ago by
Paula
▴ 10
1
vote
3
replies
272
views
How to do preprocessing from fastqc
fastqc
scRNA-seq
single-cell
updated 2 days ago by
Ram
44k • written 3 days ago by
Lulu
• 0
0
votes
1
reply
193
views
Trying to use equivalence test from a diffbind dataset
Diffbind
R
DESeq2
ChIP-seq
ATAC-seq
updated 3 days ago by
ATpoint
83k • written 3 days ago by
jandrade
• 0
2
votes
2
replies
262
views
Consistent cluster coloring
R
Seurat
2 days ago by
solo.albif
• 0
1
vote
3
replies
308
views
Slot to pull data from for DoHeatmap
DESeq2
DoHeatmap
Seurat
Pseudobulk
updated 1 day ago by
Ming Tommy Tang
★ 4.0k • written 3 days ago by
bio_info
▴ 20
117,476 results • Page
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How to convert old entrez id to updated-entrez id in R?
Answer: Example human WGS fastq data
Answer: NCBI vs Ensembl - Ortholog genes Information
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Recent Replies
Answer: How to measure pairwise genetic distance in all samples of a VCF file
by
hewm2008
▴ 40
you can try this tools :https://github.com/BGI-shenzhen/VCF2Dis
Comment: How to download a file from zenodo link without leaving terminal?
by
GenoMax
143k
You have tried to log in with one of the methods mentioned (ORCID/GitHub or a local Zenodo account) and that did not work?
Comment: BCFtools not calling variant, despite adequate coverage
by
mpiersonsmela
• 0
yes, this seems to be the problem. I will try realigning to a version of hg38 without alt contigs.
Comment: Removing batch effect in time-series data
by
Álvaro
• 0
I performed a clustered heatmap and PCA for all samples and the different timepoints did not group together. However, my doubts come from a…
Comment: BCFtools not calling variant, despite adequate coverage
by
mpiersonsmela
• 0
Strange, I wonder why. Could it have anything to do with the "chr20_KI270871v1_alt"?
Comment: BCFtools not calling variant, despite adequate coverage
by
Pierre Lindenbaum
162k
your read is discarded because mapping quality=0
Answer: Removing batch effect in time-series data
by
rfran010
▴ 960
Have you performed more formal analysis? PCA, clustering, correlation, etc... If you have a time dependent batch effect, I would expect …
Comment: BCFtools not calling variant, despite adequate coverage
by
mpiersonsmela
• 0
I uploaded the sam file here if you want to take a look: https://github.com/samtools/bcftools/issues/2211
Comment: BCFtools not calling variant, despite adequate coverage
by
mpiersonsmela
• 0
The reads are not duplicates. I think the color might be due to also matching the chr20 alt contig but I'm not sure. An example line from …
Comment: How to download a file from zenodo link without leaving terminal?
by
SlowSD
• 0
Okay, are you aware of any file access setting in zenodo by changing which this can work out?
Comment: BCFtools not calling variant, despite adequate coverage
by
mpiersonsmela
• 0
The output is: chr20 63439704 G 23 ,,,,,aa,.A.A,,a,a.aA.aA FFFFFFFFkFFFFFFFFFFFFFF
Comment: How to download a file from zenodo link without leaving terminal?
by
Pierre Lindenbaum
162k
https://zenodo.org/records/11791175 > The record is publicly accessible, but files are restricted to users with access. so, no.
Comment: Problem in input data loading in Structure
by
Mensur Dlakic
★ 27k
Error messages are usually meant to be taken literally. It says that your first line has two fewer columns than the rest of your file. It p…
Comment: How to download a file from zenodo link without leaving terminal?
by
SlowSD
• 0
Still, a 6kb html file gets downloaded in the name of SRR396636.sra_1.fastq
Comment: How to download a file from zenodo link without leaving terminal?
by
Medhat
9.7k
Could you try `wget -L -O SRR396636.sra_1.fastq "https://zenodo.org/record/11791175/files/SRR396636.sra_1.fastq"`
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