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128 results • Page
2 of 3
Sort: Votes
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Views
Votes
Replies
1
vote
4
replies
258
views
Select one microarray probe for gene (Affymetrix) - tools 2025?
Probes
Microarray
5 days ago by
Nona
▴ 90
1
vote
7
replies
332
views
Which Tool and Database for metagenomic classification at Species level with 16S
Taxonomy
16S
Amplicon
Metagenomic
5 days ago by
Aytaç
• 0
1
vote
0
replies
187
views
Tool:
ggalign: Bridging the Grammar of Graphics and Biological Multilayered Complexity
ggplot2
ggalign
updated 5 days ago by
GenoMax
149k • written 5 days ago by
Yun
▴ 60
1
vote
11
replies
1.6k
views
error to run rnammer
phylogenomics
rRNA_extraction
rnammer
updated 4 days ago by
Arslan Tariq
▴ 130 • written 13 months ago by
microorganism_001
▴ 30
1
vote
3
replies
270
views
Extract reads that didn't contribute to miRNAs following miRDeep2 analysis
miRNA
miRDeep2
small
RNA
updated 4 days ago by
GenoMax
149k • written 4 days ago by
jammydodger123456
▴ 40
1
vote
1
reply
117
views
Proteomics DEA
Proteomics
updated 22 hours ago by
ATpoint
86k • written 1 day ago by
frarodmar17
• 0
1
vote
1
reply
187
views
Blog:
Molecular Simulation: GROMACS Benchmark on 30 different GPUs on SaladCloud
Benchmark
GPU
Cloud
4 days ago by
Prashanth
▴ 10
1
vote
7
replies
2.0k
views
Convert VCF files to input file format requiered by XP-CLR1.0 software
XP-CLR
updated 4 days ago by
aqilfarooqqais267
• 0 • written 22 months ago by
Famf
▴ 30
1
vote
16
replies
698
views
Unable to get to BAM file from SAM using samtools
Samtools
BAM
SAM
updated 18 hours ago by
GenoMax
149k • written 7 days ago by
alejandro.mejiam1
▴ 20
1
vote
4
replies
722
views
CIBERSORTx error (error in rep(2, size * length(cells) -1)) : invalid 'times' argument
deconvolution
RNA-seq
CIBERSORTx
CIBERSORT
updated 9 hours ago by
zhbyrd
• 0 • written 8 months ago by
Mr. George
▴ 10
1
vote
2
replies
258
views
Machine learning for drug sensitivity prediction and signature gene
Machine-learning
drug-sensitivity
5 days ago by
qudrat.nii
▴ 40
1
vote
1
reply
184
views
Ginkgo tool for CNV
CNV
Single-cell
WGS
updated 6 days ago by
Ram
44k • written 7 days ago by
drajangirija
▴ 10
1
vote
1
reply
199
views
differential gene expression in male and female samples
CLCworkbench
RNAseq
updated 3 days ago by
ATpoint
86k • written 3 days ago by
BioS
• 0
0
votes
0
replies
17
views
Regex in umi-tools doesn't identify pattern in non-beginning positions
whitelist
UMI-Tools
UMI
UMI-TOOLS
umi-tools
1 hour ago by
kalaivani
• 0
0
votes
4
replies
325
views
Illumina HumanHT-12 V4.0 analysis but I only have the .IDAT files
Illumina
Expression-Analysis
Microarray
updated 6 days ago by
Basti
★ 2.0k • written 12 days ago by
isaac_mani
• 0
0
votes
0
replies
1
view
Annotate WGS VCF with Allele Frequencies
snpeff
vcf
wgs
allele
just now by
Gabriel
• 0
0
votes
1
reply
459
views
Can ARIBA AMR tool be tweaked to support long reads inputs (eg-Oxford Nanopore)?
AMR
Oxford
Nanopore
ARIBA
updated 6 days ago by
AHerik
▴ 20 • written 24 months ago by
varunsreeraj
• 0
0
votes
0
replies
144
views
CellChat interactions
R
CellChat
6 days ago by
solo.albif
• 0
0
votes
1
reply
184
views
Picard AddOrReplaceReadGroups,
human
illumina
libraries
picard
updated 6 days ago by
Pierre Lindenbaum
165k • written 6 days ago by
María José
▴ 10
0
votes
0
replies
846
views
How can I linearize certain segments within an existing protein structure constraining to volumetric grids using PyMOL scripting?
python
protein-structure
structural-bioinformatics
protein
6 days ago by
Aman Vishwakarma
▴ 10
0
votes
1
reply
166
views
Converting SRA Data to FASTQ and Saving Directly to S3
sra-toolkit
AWS
SRA
S3
updated 6 days ago by
GenoMax
149k • written 6 days ago by
Soohyun
• 0
0
votes
1
reply
210
views
How to obtain spliced and unspliced counts from parse biosciences generated count data ?
scrnaseq
transcriptomics
single-cell
updated 6 days ago by
Bastien Hervé
6.1k • written 6 days ago by
shome
▴ 10
0
votes
2
replies
219
views
Unexpected behavior of `vg surject`
surject
vg
6 days ago by
Ilya
• 0
0
votes
1
reply
308
views
Data Normalization of RNA-seq gene expression
TMM
classification
MetastasisRNA-Seq
updated 5 days ago by
Ram
44k • written 8 days ago by
maryak
▴ 20
0
votes
1
reply
173
views
HaplotypeCaller Not Detecting Variants
GATK
Variantcalling
WGS
updated 5 days ago by
GenoMax
149k • written 5 days ago by
akshit
• 0
0
votes
2
replies
197
views
PDX RNA seq counts
counts
RNAseq
PDX
5 days ago by
ChumBucket2024
• 0
0
votes
3
replies
1.5k
views
STARsolo parameters for 10X Multiome kit (scRNA-seq & scATAC-seq)
scRNA-seq
scATAC-seq
STARsolo
10X_Multiome
Xenopus
updated 5 days ago by
tranhangk15cnsh
• 0 • written 2.7 years ago by
thanospas
• 0
0
votes
0
replies
159
views
Help understanding best binning practices
binning
viruses
metagenome
contigs
5 days ago by
boone5jones
• 0
0
votes
0
replies
154
views
Reconstruction of ancestral phenotypes
phenotypes
5 days ago by
1473989647
• 0
0
votes
0
replies
161
views
Issue with Taxonomy Assignment Using Kraken and Custom Database (BOLD, Nemabiome) in QIIME2 shotgun
BOLD
Qiime2
Taxonomy
Assignment
Kraken2
5 days ago by
ohtang7
▴ 40
0
votes
0
replies
160
views
CIBERSORTx error when running sc-RNA seq reference dataset
cibersortx
cibersort
5 days ago by
zhbyrd
• 0
0
votes
0
replies
155
views
pseudobulks on patch-seq
edgeR
patch-seq
DESeq2
pseudobulks
5 days ago by
yves33
• 0
0
votes
3
replies
277
views
Should I Use p-value or Adjusted p-value for Differential Methylation Analysis (Illumina EPIC v2)?
DNAMethylation
IlluminaEPICv2
DifferentialMethylationAnalysis
updated 5 days ago by
i.sudbery
21k • written 5 days ago by
Srinka
▴ 20
0
votes
1
reply
210
views
Unicycler error
human
illumina
libraries
unicycler
updated 5 days ago by
Arup Ghosh
3.3k • written 5 days ago by
María José
▴ 10
0
votes
1
reply
1.1k
views
News:
FINAL CALL - Single-Cell RNA-Seq Data Analysis: A Practical Introduction (March 17-19, 2025 in Berlin, Germany)
transcriptomics
scRNAseq
singleCell
5 days ago by
ecSeq Bioinformatics
▴ 10
0
votes
1
reply
199
views
MuSE sump: Segmentation fault (core dumped)
error
MuSE
core
somatic
sump
dump
updated 4 days ago by
Arup Ghosh
3.3k • written 5 days ago by
Marie
• 0
0
votes
1
reply
243
views
Eigencor plot after limma::removeBatchEffect
DESeq2
PCAtools
updated 4 days ago by
jared.andrews07
★ 18k • written 4 days ago by
f2ff7a46
• 0
0
votes
1
reply
1.8k
views
MToolBox VCF output error
SNP
software error
next-gen
updated 4 days ago by
adarsh_munna
▴ 50 • written 8.3 years ago by
waqasnayab
▴ 250
0
votes
1
reply
239
views
Job:
Job: Bioinformatics Postdoc Position at Columbia University
aging
single-cell
4 days ago by
Qinghua
• 0
0
votes
0
replies
191
views
Job:
Ad Astra Fellow – Assistant Professor of Artificial Intelligence in Medical Data Analytics
data-analytics
assistant-professor
medicine
AI
4 days ago by
Colm
• 0
0
votes
0
replies
145
views
XP-CLR input files
XPCLR
updated 4 days ago by
GenoMax
149k • written 4 days ago by
aqilfarooqqais267
• 0
0
votes
8
replies
378
views
Bowtie2 keeps exiting with "Error reading _plen[] array:"
bowtie2
updated 3 days ago by
GenoMax
149k • written 3 days ago by
biobaker
• 0
0
votes
1
reply
246
views
Figures and plots for integration of ATAC and RNA seq data
ATAC-seq
RNA-seq
updated 3 days ago by
jared.andrews07
★ 18k • written 4 days ago by
SpartanII
• 0
0
votes
1
reply
229
views
Issue with Converting Excel Data to JSON
python
classifier
json
machine-learning
updated 3 days ago by
natasha.sernova
★ 4.0k • written 3 days ago by
Cake Day
• 0
0
votes
0
replies
144
views
News:
Online Course: Machine Learning Methods for Longitudinal Data with Python
Longitudinal-Data
Machine-Learning
Deep-Learning
Omics
updated 2 days ago by
Ram
44k • written 3 days ago by
Physalia-courses
★ 2.6k
0
votes
0
replies
177
views
News:
course: Generalised Linear Models in R - Online, 24–28 February.
R
Generalised-Linear-Models
GLM
updated 2 days ago by
Ram
44k • written 3 days ago by
Physalia-courses
★ 2.6k
0
votes
2
replies
245
views
Sample replicate for transcriptomic
replicate
transcriptomic
Sample
magna
daphnia
2 days ago by
Jane
• 0
0
votes
2
replies
254
views
Error in running MToolBox
NGS
Variant-Calling
MToolBox
Mitochondria
2 days ago by
adarsh_munna
▴ 50
0
votes
2
replies
156
views
clinker, a gene cluster visualization tool, crashed its online site
cluster
gene
updated 2 days ago by
ATpoint
86k • written 2 days ago by
yinfang
• 0
0
votes
1
reply
192
views
Finding target for the biologically active compound
target-prediction
updated 2 days ago by
dthorbur
★ 2.7k • written 2 days ago by
Pragya
• 0
128 results • Page
2 of 3
Recent Votes
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Comment: How to extract fasta sequences from assembled transcripts generated by Stringtie
by
Juke34
9.1k
I do not know if the problem is related but if your genome is already masked you should let all the option empty: ``` #-----Repeat Masking…
Comment: How to extract fasta sequences from assembled transcripts generated by Stringtie
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▴ 170
Thank you @juke34 , I used agat for convert my gtf. Sorry, I have other doubt, I'm starting with plant annotation and I'm using maker for t…
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colindaven
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It is a read multimapping problem - bowtie1 (?) likely considers these repetitive and filters them out. Your mistake was to combine all 3 r…
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fyi, the SRA-explorer is a third-party tool, not one from NCBI.
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Dear Pierre, If one set of gvcf files are ISAAC aligned (>80,000 samples) and the other DRAGEN (100 samples) as discussed above but I hav…
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Hi Rory will you help me out about the plot issue? > dba.plotProfile(dbObj5) Generating report-based DBA object... Generat…
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Titus
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Hi, may be this could help you : https://github.com/ncbi/sra-tools/issues/531 Best
Comment: How to extract fasta sequences from assembled transcripts generated by Stringtie
by
Juke34
9.1k
Sorry yes if it’s a GTF you have to convert to GFF. But it was long time ago maybe recent version allows to use GTF directly?
Comment: CIBERSORTx error (error in rep(2, size * length(cells) -1)) : invalid 'times' ar
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zhbyrd
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Hi Amairani! I was wondering if you resolved it at all?
Answer: CIBERSORTx error (error in rep(2, size * length(cells) -1)) : invalid 'times' ar
by
zhbyrd
• 0
Hi, George! I am also having the same problem. i was wondering if you have found a solution. Thank you.
Comment: How to extract fasta sequences from assembled transcripts generated by Stringtie
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Thank you for you answer @juke34 , so it is not necessary convert to the gtf from StringTie to GFF o maybe use agat_convert_sp_gxf2gxf.pl f…
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If you're using a BSD Unix (macOS etc.) their `sort` may include other options, such as `--mergesort`. It also includes `--mmap`, which can…
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sounds like a great oppor-tuna-ty. you guys are krilling it!
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