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679 results • Page
8 of 14
Sort: replies
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Views
Votes
Replies
1
vote
2
replies
327
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
18 days ago by
Nafi
• 0
0
votes
2
replies
344
views
Job:
Bioinformatics Analyst - Laboratory Medicine and Pathology
job
updated 13 days ago by
Xiaofen
• 0 • written 13 days ago by
toddknutson
▴ 60
0
votes
2
replies
161
views
seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from input file
subseq
seqtk
extractionproblem
10 hours ago by
KHURRAM SHAHZAD
• 0
1
vote
2
replies
294
views
News:
We created a Bioinformatics Competition for Spatial Transcriptomics: MICOS-EU
cell-clustering
Spatial-transcriptomics
updated 12 days ago by
Weiwen
• 0 • written 13 days ago by
MICOS
▴ 10
0
votes
2
replies
189
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
6 days ago by
IdaHao0921
• 0
0
votes
2
replies
236
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
7 days ago by
analyst
▴ 50
1
vote
2
replies
391
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign
cell-markers
22 days ago by
Francesco
▴ 10
2
votes
2
replies
371
views
Association study using SNP data
Association
Allele
Parentage
SNP
14 days ago by
drajangirija
• 0
3
votes
2
replies
430
views
Extract protein sequence
fasta
alignment
blast
19 days ago by
anna
▴ 20
2
votes
2
replies
2.6k
views
Pindel Segmentation Fault Error
pindel
updated 15 days ago by
Ruqaiya
• 0 • written 10.3 years ago by
Yuelin
▴ 20
0
votes
2
replies
205
views
Phasing a mixture of two individuals' DNA with long reads
long-reads
phasing
11 days ago by
njornet
▴ 20
0
votes
2
replies
756
views
homer not configured properly
Homer
makeTagDirectory
updated 17 days ago by
clairechung112
• 0 • written 24 months ago by
amahdi779
• 0
0
votes
2
replies
244
views
Obtaining Infinium Methylation450K manifest for hg38
TCGA
hg38
methylation
Illumina
updated 7 days ago by
Zhenyu Zhang
★ 1.2k • written 11 days ago by
elisheva
▴ 120
2
votes
2
replies
261
views
Server or aws cloud- which one is better for gatk pipeline
aws
server
calling
gatk
cloud
updated 10 days ago by
Michael
54k • written 11 days ago by
ashaneev07
▴ 20
14
votes
2
replies
7.1k
views
Trouble with Pilon installation
polishing
pilon
installation
updated 25 days ago by
Lissa Cruz Saavedra
• 0 • written 7.3 years ago by
Rox
★ 1.4k
0
votes
2
replies
315
views
Annovar using R package
Annovar
gnomAD
R
24 days ago by
DKA
▴ 40
1
vote
2
replies
286
views
RNA-seq data for deep learning classification
rna-seq
16 days ago by
yahn
• 0
1
vote
2
replies
284
views
alignment result
RNA-seq
samtools
hisat2
25 days ago by
ahmad.sajad4541
• 0
1
vote
2
replies
1.7k
views
Seurat CellCycleScoring – confused about the proper order of operations when using SCTransform
CellCycleScoring
SCTransform
Seurat
updated 11 days ago by
Li
• 0 • written 2.3 years ago by
GPM
▴ 10
2
votes
2
replies
206
views
genome finishing
finishing
genome
updated 4 days ago by
nd48
▴ 20 • written 4 days ago by
trezini
• 0
0
votes
2
replies
236
views
Presence of unknown sites in ANNOVAR output file
ANNOVAR
updated 9 days ago by
Ram
43k • written 10 days ago by
sainavyav22
• 0
7
votes
2
replies
333
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 26 days ago by
geneontologyhelp
▴ 400 • written 27 days ago by
catherine.teyssier
• 0
0
votes
2
replies
251
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
17 days ago by
dtnondorf
• 0
2
votes
2
replies
205
views
Is therer any suggestions on mapping rate of WGBS data?
mapping
read
alignment
WGBS
12 days ago by
Zeng Jingyu
▴ 60
2
votes
2
replies
193
views
Cannot install bwa-mem2 via conda
conda
mamba
python
updated 3 days ago by
Ram
43k • written 4 days ago by
jsmith120f
• 0
1
vote
2
replies
213
views
Alphafold 3 pLDDT coloring scheme in chimerax?
ChimeraX
Alphaphold
Alphaphold3
updated 5 days ago by
colindaven
6.4k • written 5 days ago by
mbrav005
• 0
2
votes
2
replies
490
views
Using vg gamsort with naive sorting algorithm
gamsort
vg
updated 26 days ago by
Pierre Lindenbaum
161k • written 8 months ago by
AshleeThomson
▴ 80
1
vote
2
replies
305
views
read length in structural variant calling
nanopore
SV
QC
ONT
variant
16 days ago by
eebloom
▴ 80
2
votes
2
replies
251
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
updated 20 days ago by
GenoMax
142k • written 21 days ago by
Winter
• 0
0
votes
2
replies
376
views
How to update R on ubuntu
installation
update
R
apt-get
20 days ago by
Bosberg
▴ 50
1
vote
2
replies
297
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
18 days ago by
rianna.collins
• 0
0
votes
2
replies
250
views
What should I consider as FASTA for dataset?
PDB
FASTA
20 days ago by
Nafi
• 0
0
votes
1
reply
163
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Cancer-Research
ATAC-seq
updated 6 days ago by
Ram
43k • written 13 days ago by
David
• 0
2
votes
1
reply
237
views
Failed to open VCF file
GATK
sentieon
BWA-MEM
updated 8 days ago by
Pierre Lindenbaum
161k • written 9 days ago by
melissachua90
▴ 70
0
votes
1
reply
199
views
metagenomic virome quality assessment
viromics
metagenomics
updated 20 days ago by
Ram
43k • written 20 days ago by
Petchimuthu
• 0
2
votes
1
reply
216
views
RNAseq coverage vs depth for transcript isoform expression?
RNAseq
updated 1 day ago by
Gordon Smyth
★ 7.2k • written 2 days ago by
marineandriot
• 0
0
votes
1
reply
163
views
Manual Assembly and Protein Translation, HELP, assignment revision
sequence
university
assembly
protein
genomics
updated 7 days ago by
Philipp Bayer
8.5k • written 7 days ago by
samRayne
• 0
0
votes
1
reply
166
views
How to process Bulk WES data?
WES
WGS
updated 6 days ago by
GenoMax
142k • written 6 days ago by
wyuan37
• 0
0
votes
1
reply
209
views
extract viral protein of interest from 10k whole viral genomes
nBLAST
viral-genome
updated 9 days ago by
Ram
43k • written 9 days ago by
Shwetha
• 0
2
votes
1
reply
350
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
updated 16 days ago by
chrchang523
10k • written 20 days ago by
8armed
▴ 10
0
votes
1
reply
371
views
Snakemake fails to find conda in PBS
snakemake
updated 10 days ago by
tim.booth
▴ 60 • written 5 weeks ago by
yixinzeng
• 0
7
votes
1
reply
213
views
Tutorial:
removeBatchEffect explained using base R linear models
limma
effects
batch
removebatcheffects
updated 12 days ago by
dariober
14k • written 12 days ago by
nhaus
▴ 360
0
votes
1
reply
4
views
How to hide label in layout file of MCscan (python version)
MCscan
7 minutes ago by
jinyi
• 0
0
votes
1
reply
62
views
Functional enrichment analysis for unique gene IDs
RNA-SEQ
updated 3 hours ago by
ATpoint
82k • written 5 hours ago by
Pegasus
▴ 100
0
votes
1
reply
159
views
input file for alternative splicing in rmats in linux
rmats
updated 10 days ago by
Ram
43k • written 10 days ago by
Lambodarswain316
• 0
4
votes
1
reply
270
views
LD-prune variants while maintaining a list of SNPs
snp
vcf
plink
filtering
independent
updated 14 days ago by
zx8754
11k • written 15 days ago by
Jautis
▴ 560
0
votes
1
reply
52
views
Error in using BioSampleParser tool: subscript out of bounds
R
updated 44 minutes ago by
marco.barr
▴ 130 • written 8 hours ago by
Mohamed Samir
▴ 20
0
votes
1
reply
324
views
DMRcate ranges liftover hg19 to hg38
DMRcate
Liftover
DMR
Methylation
annotation
updated 14 days ago by
aaron.stevens
• 0 • written 3 months ago by
sativus
▴ 20
1
vote
1
reply
175
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
updated 20 days ago by
GenoMax
142k • written 21 days ago by
Ruqaiya
• 0
1
vote
1
reply
303
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 1 day ago by
nguyenn6
• 0 • written 3 months ago by
star
▴ 10
679 results • Page
8 of 14
Recent Votes
Answer: Q: GenomeScope input and how to interpret the results
Answer: How to find tandem duplications pattern in a DNA sequence
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Sequence alignment on split read event such as inversion, duplication and complex nested events.
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Recent Replies
Comment: GO analysis: p-value range
by
sooni
▴ 20
When I run the code, the following message appears: Scale for y is already present. Adding another scale for y, which will replace…
Comment: Why most genes have high padj values
by
mnx0723
• 0
In the case of other samples, the total number of genes is at least 3,000 more than that one, but it seems to be a relatively small number.…
Comment: How to hide label in layout file of MCscan (python version)
by
jinyi
• 0
Command line is as follows: python -m jcvi.graphics.synteny Cs.Cm.i1.blocks Cs_Cm.bed layout2.txt
Comment: Add stats to the plot
by
marco.barr
▴ 130
Thank you, it seems to be clearer. Your Condition already has two factorial levels. You can replace these names in groups 1 and 2. da…
Comment: Error in using BioSampleParser tool: subscript out of bounds
by
marco.barr
▴ 130
Hi, I also had the same problem. If you check its github page there have been no releases for many years and these errors cannot be fixed. …
Comment: Add stats to the plot
by
Ghada
• 0
Thanks, thats really helpful ![enter image description here][1] ![enter image description here][2] [1]: /media/images/0470f3dc-5945-…
Comment: PCA Visualization error in R
by
marco.barr
▴ 130
SNPRelate is an R package that is able to read from VCF files directly and perform PCA and IBD/IBS. See the documentation for details in Bi…
Comment: Why most genes have high padj values
by
ATpoint
82k
788 differential genes is a lot. What is the problem?
Comment: Why most genes have high padj values
by
mnx0723
• 0
Sorry, I made edits.
Comment: Why most genes have high padj values
by
Pierre Lindenbaum
161k
Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the cod…
Comment: GO analysis: p-value range
by
marco.barr
▴ 130
Try adding: `scale_y_continuous(breaks=seq(0, max_count, by=0.05))`
Comment: Functional enrichment analysis for unique gene IDs
by
ATpoint
82k
If these genes do not have a symbol then it is utterly unlikely that anyone has looked at their function. I would get their Ensembl IDs and…
Comment: Add stats to the plot
by
marco.barr
▴ 130
The error is likely due to the fact that the structure of your data in data4.ts and data2.ts may not contain the Condition values. The grou…
Comment: How to find identical sequences in genome fasta file (by Python or any possible
by
Pierre Lindenbaum
161k
+ https://www.biostars.org/p/3003/ + https://www.biostars.org/p/9550118/ + https://www.biostars.org/p/158148/
Answer: How to find tandem duplications pattern in a DNA sequence
by
micah
▴ 30
I built a web application can directly find repeat unit and repeat times, try it at http://64.64.240.35:8050/. ![Dot plot][1] ![5 tandem …
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