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119,839 results • Page
1 of 2397
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0
votes
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332
views
Clarification on StringTie's `--merge` parameters
stringtie
stringtie-merge
updated 40 minutes ago by
cpw
• 0 • written 7 months ago by
DGTool
▴ 290
0
votes
0
replies
5
views
Spam:
8XBet
8XBet
1 hour ago by
casinox08
0
0
votes
0
replies
6
views
Spam:
sv88party
sv88party
1 hour ago by
SV88 - Khám Phá Các Game Đổi Thưởng và…
0
1
vote
8
replies
185
views
Tools for Subsampling Paired-End Reads to 25X Coverage ?
paired-end
fastq
depth
sequencing
coverage
updated 1 hour ago by
Mensur Dlakic
★ 28k • written 9 hours ago by
Sony
▴ 20
3
votes
3
replies
3.4k
views
6 follow
GeneActivity without Fragments file in Seurat for Integrating scRNA-seq and scATAC-seq
ATAC
Fragments
GeneActivity
RNA
Seurat
updated 5 hours ago by
Mr
• 0 • written 2.5 years ago by
el24
▴ 50
4
votes
8
replies
2.2k
views
hd WGCNA - Preservation statistics (Zsummary & MedianRank)
hdWGCNA
WGCNA
updated 5 hours ago by
Nils
• 0 • written 2.0 years ago by
AKypR
▴ 10
0
votes
0
replies
37
views
No overlapping contigs problem
virus
haplotypecaller
gatk
6 hours ago by
Matheus
• 0
821
votes
169
replies
161k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 12 weeks ago by
Biostar
3.2k • written 8.0 years ago by
Istvan Albert
102k
4
votes
4
replies
171
views
undermined fastq and top unknown barcodes
bcl2fastq
5 hours ago by
1769mkc
★ 1.2k
3
votes
1
reply
91
views
Problem while replicating methylation predicting paper, looking for explanation
bioconductor
methylation
machine-learning
r
updated 6 hours ago by
cmdcolin
★ 4.0k • written 7 hours ago by
Junk
• 0
0
votes
0
replies
35
views
ssGSEA cross-species
ssGSEA
RNAseq
TPM
GSEA
7 hours ago by
georgii.vdovin
• 0
3
votes
5
replies
147
views
Batch correction of two RNA-Seq data sets
DESeq2
batch-correction
updated 6 hours ago by
Ram
44k • written 9 hours ago by
gogeni5529
▴ 50
0
votes
0
replies
45
views
Plot meRIP bw data on single RNA
plot
meRIP
updated 6 hours ago by
Ram
44k • written 11 hours ago by
jia
• 0
1
vote
1
reply
98
views
Optimal Method for Chain File Generation: BLAT vs Minimap2 and MAF2Chain vs axtChain
Generation
paf2chain
axtChain
Tool
Chain
updated 5 hours ago by
cmdcolin
★ 4.0k • written 13 hours ago by
myoui3122010
▴ 30
2
votes
6
replies
368
views
Which method should I use to merge scRNA-seq data, Cellranger aggr or Seurat?
scRNA-seq
CellRanger
hdWGCNA
Seurat
updated 6 hours ago by
Ram
44k • written 2 days ago by
Apprentice
▴ 170
0
votes
0
replies
52
views
Clonality dendrogram evolution
clonality
ClonEvol
dendrogram
14 hours ago by
alba
• 0
2
votes
1
reply
126
views
What laptop specifications should I consider as a Bioinformatics PhD student with HPC access?
Laptop
hpc
cluster
updated 6 hours ago by
Ram
44k • written 14 hours ago by
Tundup
• 0
0
votes
2
replies
525
views
News:
7 days left: Special Deal - 15% Off - RNA-Seq Data Analysis Workshop (March 24 - 27, 2025 in Halle, Germany)
Transcriptomics
splicing
differential-expression
RNA-Seq
updated 6 hours ago by
Ram
44k • written 18 days ago by
ecSeq Bioinformatics
• 0
0
votes
1
reply
82
views
VCF Merge
VCF
MergeSTR
updated 16 hours ago by
Pierre Lindenbaum
164k • written 16 hours ago by
Muhammad
• 0
0
votes
3
replies
210
views
Script that should show if the position of an indel is within the range of a miRNA is creating empty files. Could you help me?
miRNA
indel
updated 6 hours ago by
Ram
44k • written 1 day ago by
jhonatan.henrique
• 0
1
vote
1
reply
355
views
Issues with RAT in CAT_pack and Optimizing Relative Abundance Calculation
metagenomics
taxonomy
mag
annotation
updated 1 day ago by
mks002
▴ 220 • written 9 weeks ago by
LuciaNhu
▴ 10
0
votes
1
reply
120
views
Hi-C interactions significance
chromatin
interactions
pvalue
Hi-C
significance
updated 1 day ago by
hamarillo
▴ 80 • written 1 day ago by
Helena
• 0
3
votes
4
replies
353
views
Conceptual and statistical help in creating a synthetic RNAseq cohort from a real-world cohort of samples
statistics
DESeq2
RNAseq
updated 11 hours ago by
ATpoint
86k • written 3 days ago by
K.patel5
▴ 150
0
votes
0
replies
83
views
StringTie error
DE
RNA-seq
StringTie
updated 6 hours ago by
Ram
44k • written 1 day ago by
SHN
▴ 40
0
votes
0
replies
80
views
A problem with a plink file made from a VCF
plink
vcf
1 day ago by
HoWI
• 0
1
vote
2
replies
150
views
Annotating bacterial intergenic regions
bacteria
gene
intergenic
annotation
updated 15 hours ago by
dthorbur
★ 2.6k • written 1 day ago by
Gio
• 0
0
votes
0
replies
80
views
KEGGREST to retrieve some data from KEGG
genes
keggLink
1 day ago by
mrashad
▴ 80
1
vote
1
reply
138
views
Creating adjacency matrix from collapsed row values in R
adjacency
reshape2
matrix
r
1 day ago by
ARP
• 0
0
votes
4
replies
203
views
Blast with variable number of Ns
blast
6 hours ago by
samuel.himes
• 0
1
vote
5
replies
401
views
Deducing AIRR-seq Library Generation From SRA Data
generation
SRA
airflow
primer
airrflow
1 day ago by
A Soggy Waffle
• 0
2
votes
1
reply
164
views
BWA align in human and parasite genome, and sort them
BWA
updated 1 day ago by
GenoMax
148k • written 1 day ago by
Bender
• 0
1
vote
3
replies
202
views
Use of "grep" in RNAseq trimming
RNAseq
PolyA
updated 1 day ago by
GenoMax
148k • written 1 day ago by
Luna_1215
• 0
1
vote
3
replies
245
views
Could someone send me CISA software ?
CISA
updated 6 hours ago by
Ram
44k • written 1 day ago by
lu_baicheng
• 0
0
votes
1
reply
133
views
Download metabolic information from databases using the NCBI Taxonomy ID
metabolism
database
R
taxonomy
ncbi
updated 1 day ago by
GenoMax
148k • written 1 day ago by
ThaiosX195
• 0
0
votes
1
reply
112
views
No change in quality score graph even after adapter removal
rna-seq
fastqc
Trimmomatic
updated 1 day ago by
dsull
★ 7.0k • written 1 day ago by
Sreedevi
• 0
0
votes
1
reply
110
views
Regarding ClinVar's VCF file
matrix
disease
vcf
clinvar
gene
updated 11 hours ago by
Jeremy Leipzig
22k • written 1 day ago by
singhankit973
• 0
4
votes
9
replies
309
views
Single-cell dimensionality reduction and clustering
Seurat
updated 9 hours ago by
yura.grabovska
▴ 690 • written 1 day ago by
xingyu
▴ 10
0
votes
0
replies
85
views
How to load series matrix file into SeSAMe or minfi for processing?
sesame
geo
illumina
minfi
machine-learning
updated 1 day ago by
Ram
44k • written 1 day ago by
Junk
• 0
0
votes
1
reply
149
views
Plant diploid genome, phashed, CLR reads, PECAT
diploid
genome
Phased
23 hours ago by
sansan96
▴ 130
4
votes
14
replies
2.6k
views
7 follow
Is there anyone who downloaded Azimuth packges?
Azimuth
scRNAseq
updated 1 day ago by
ATpoint
86k • written 9 months ago by
kayah
▴ 20
3
votes
10
replies
423
views
Error in conversion of ensembl to gene names
Ensembl
BioMart
updated 1 day ago by
Istvan Albert
102k • written 2 days ago by
anasjamshed
▴ 140
1
vote
1
reply
372
views
Tool:
CellLocator: An Open-Source Tool for Unlocking Deeper Insights from Live-Cell Imaging
open-source
deep-learning
denoising
single-cell
incucyte
2 days ago by
Michael
▴ 10
0
votes
3
replies
234
views
Which data to choose for correlation examination
correlation
WGCNA
TPM
batch
spearman
2 days ago by
lyan125
▴ 10
4
votes
12
replies
476
views
Transcript coverage 3' bias. Is it really that determining?
mappings
transcriptome
RNA
updated 1 day ago by
i.sudbery
20k • written 2 days ago by
Amb@r85
▴ 10
3
votes
7
replies
579
views
Quantify miRNAs from whole transcriptome library (single end, TruSeq, 100bp)
miRNA
whole-transcriptome-TruSeq
updated 2 days ago by
i.sudbery
20k • written 4 months ago by
w.denhollander
• 0
0
votes
1
reply
194
views
comparing STARsolo UMI-based directional deduplication vs umi-tools?
single-cell
starsolo
deduplication
umi-tools
updated 2 days ago by
i.sudbery
20k • written 3 days ago by
mk
▴ 310
0
votes
0
replies
128
views
Prediction of sRNA in FASTA file
FASTA
Prediction
sRNA
2 days ago by
nashwaabdulrasheed09
• 0
0
votes
0
replies
123
views
Identification of SSR markers from RNA-seq data
MISA
SSR-markers
data
RNA-seq
2 days ago by
Kutti
• 0
0
votes
8
replies
566
views
Super enhancer calling using ROSE for mm39 genome: list index out of range error
ChIP-Seq
super-enhancers
ROSE
mm39
updated 1 day ago by
jared.andrews07
★ 18k • written 4 days ago by
Gayatri
• 0
0
votes
1
reply
175
views
assembling human mitochondrial genomes with nanopore long reads
ONT
assembly
genome
mitochondria
nanopore
2 days ago by
eebloom
▴ 90
119,839 results • Page
1 of 2397
Recent Votes
Comment: Tools for Subsampling Paired-End Reads to 25X Coverage ?
Answer: GeneActivity without Fragments file in Seurat for Integrating scRNA-seq and scAT
GeneActivity without Fragments file in Seurat for Integrating scRNA-seq and scATAC-seq
Answer: undermined fastq and top unknown barcodes
Answer: Problem while replicating methylation predicting paper, looking for explanation
Answer: Problem while replicating methylation predicting paper, looking for explanation
Answer: Problem while replicating methylation predicting paper, looking for explanation
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Recent Replies
Answer: Clarification on StringTie's `--merge` parameters
by
cpw
• 0
Hello @dgtool did you ever work this out? I am having the same problem as I only want the reference transcripts to be included if they ar…
Comment: Tools for Subsampling Paired-End Reads to 25X Coverage ?
by
Mensur Dlakic
★ 28k
In my hands, `bbnorm.sh` has been faster but `khmer` downsampling has given better assemblies.
Comment: Tools for Subsampling Paired-End Reads to 25X Coverage ?
by
GenoMax
148k
BBTools also includes `bbnorm.sh`. $ bbnorm.sh Written by Brian Bushnell Last modified October 19, 2017 Descript…
Comment: scATAC-seq workflow
by
Mr
• 0
If you are looking for something straightforward, clearly bioinformatics is the wrong field :D
Answer: Tools for Subsampling Paired-End Reads to 25X Coverage ?
by
Mensur Dlakic
★ 28k
As you were told already, the BBMap suite can downsample the reads to a desired coverage. However, to the best of my knowledge this is rand…
Answer: GeneActivity without Fragments file in Seurat for Integrating scRNA-seq and scAT
by
Mr
• 0
Signac retiring the CreateGeneActivityMatrix was a really bad choice as there are lots of GEO datasets without fragment files
Comment: Optimal Method for Chain File Generation: BLAT vs Minimap2 and MAF2Chain vs axtC
by
cmdcolin
★ 4.0k
I necessarily can't speak to what are the best options, but it could be worth trying out some easy to run pipelines like LiftOn (https://gi…
Comment: undermined fastq and top unknown barcodes
by
1769mkc
★ 1.2k
304 samples what I see in the samplesheet what I got ," How many index pairs do you have in the fastq, assuming you can distinguish the re…
Comment: hd WGCNA - Preservation statistics (Zsummary & MedianRank)
by
Nils
• 0
I’m wondering why I’m getting two different Zsummary.qual results, even though I used the same reference network. I thought Zsummary.qual i…
Answer: undermined fastq and top unknown barcodes
by
swbarnes2
14k
How many samples do you have? How many index pairs do you have in the fastq, assuming you can distinguish the real pairs from noise? A…
Comment: Assigning taxonomic features in CAT: incorrect species annotation?
by
mks002
▴ 220
Hi, You are saying why genus and family level assignment is not showing up? As Bayer pointed about how the sequenced genome was submitte…
Answer: Problem while replicating methylation predicting paper, looking for explanation
by
cmdcolin
★ 4.0k
here is the output from google gemini when I ask it to translate the sentence to more plain english: > "This sentence is explaining a da…
Comment: Could someone send me CISA software ?
by
Ram
44k
Find an alternative. Or reach out to the developers and take on maintenance responsibility.
Comment: Blast with variable number of Ns
by
samuel.himes
• 0
Yeah, my two known sequences are long enough to blast on their own. Up to this point, we actually have been blasting them separately. What …
Comment: Batch correction of two RNA-Seq data sets
by
i.sudbery
20k
Given you have sperate wildtypes from the eaceh of the two batches, and the only comparisons you are likely to make are Treatment vs wildty…
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