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183 results • Page
3 of 4
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1.3k
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Extracting named fasta sequences according to list with Biopython
Biopython
FASTA
updated 4 days ago by
Rubayetul
• 0 • written 2.6 years ago by
lachiemck
• 0
0
votes
2
replies
303
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 5 days ago by
Zhenyu Zhang
★ 1.2k • written 14 days ago by
yahn
• 0
0
votes
2
replies
232
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
5 days ago by
analyst
▴ 50
0
votes
2
replies
210
views
Output file of samtools flagstat empty
samtools-flagstat
updated 5 days ago by
colindaven
6.4k • written 5 days ago by
ramendra.sarma
• 0
1
vote
2
replies
208
views
Alphafold 3 pLDDT coloring scheme in chimerax?
ChimeraX
Alphaphold
Alphaphold3
updated 3 days ago by
colindaven
6.4k • written 3 days ago by
mbrav005
• 0
0
votes
2
replies
179
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
4 days ago by
IdaHao0921
• 0
0
votes
2
replies
189
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
3 days ago by
melissa.joubert
• 0
0
votes
2
replies
151
views
Trimming tool
Trimmer
tool
updated 13 hours ago by
ntsopoul
▴ 60 • written 15 hours ago by
GeneC
• 0
0
votes
2
replies
433
views
News:
FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last places available
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
4 days ago by
David Langenberger
11k
1
vote
1
reply
222
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
updated 3 days ago by
dariober
14k • written 4 days ago by
Holly
▴ 10
0
votes
1
reply
146
views
Polish a large genome with Pilon
Pilon
Pacbio
Polish
Illumina
3 days ago by
sansan_96
▴ 90
0
votes
1
reply
161
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 4 days ago by
GenoMax
142k • written 4 days ago by
cedric.blais
• 0
0
votes
1
reply
161
views
How to process Bulk WES data?
WES
WGS
updated 4 days ago by
GenoMax
142k • written 4 days ago by
wyuan37
• 0
0
votes
1
reply
247
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Mendelian-Randomization
updated 4 days ago by
Ram
43k • written 8 days ago by
Nikki
• 0
0
votes
1
reply
148
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Cancer-Research
ATAC-seq
updated 4 days ago by
Ram
43k • written 11 days ago by
David
• 0
0
votes
1
reply
139
views
Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
annotation
vcf
vep
zygosity
deepvariant
2 days ago by
asalimih
▴ 60
0
votes
1
reply
142
views
Splitting Seurat object by sample layers
seurat
updated 4 days ago by
Ram
43k • written 4 days ago by
kilcdincer
▴ 10
0
votes
1
reply
151
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences
Demuxlet
updated 4 days ago by
Ram
43k • written 4 days ago by
eking28
• 0
0
votes
1
reply
113
views
Design for complex RNA-Seq experiment using Deseq2
Model.Matrix
RNA-Seq
Limma
DESeq2
edgeR
updated 11 hours ago by
swbarnes2
14k • written 15 hours ago by
Ezequiel
• 0
1
vote
1
reply
242
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
2 days ago by
ramiro.barrantes
• 0
0
votes
1
reply
162
views
consensus sequence calling
consensus
updated 4 days ago by
bk11
★ 2.5k • written 4 days ago by
Ghada
• 0
0
votes
1
reply
571
views
scRNAseq quality control weird double curve in nFeature vs nCount plot
scRNA-seq
QC
single
cell
BDRhapsody
analysis
updated 2 days ago by
valdirbarth
▴ 20 • written 12 months ago by
Salomé
• 0
0
votes
1
reply
173
views
What's next after GATK variant calling pipeline?
GATK
pipeline
figures
DNA-seq
updated 2 days ago by
Michael
54k • written 2 days ago by
mgranada3
▴ 30
0
votes
1
reply
164
views
perseus software (version 1.5.5)
preseus
mass
spectrometry
data
updated 1 day ago by
DGTool
▴ 20 • written 3 days ago by
iqra
• 0
0
votes
1
reply
148
views
Seurat v5 and how to correctly integrate across multiple experiments
Seurat
scRNA
R
updated 1 day ago by
Papyrus
★ 2.9k • written 2 days ago by
yura.grabovska
▴ 90
0
votes
1
reply
157
views
Mouse ribosome sequences in fasta format
fasta
mm10
rRNA
updated 4 days ago by
GenoMax
142k • written 5 days ago by
octpus616
▴ 100
0
votes
1
reply
150
views
Difference in number of reads when using duplex and simplex base calling with Dorado
base
calling
nanopore
simplex
dorado
duplex
updated 1 day ago by
GenoMax
142k • written 2 days ago by
Lélé
▴ 10
2
votes
1
reply
234
views
Failed to open VCF file
GATK
sentieon
BWA-MEM
updated 6 days ago by
Pierre Lindenbaum
161k • written 7 days ago by
melissachua90
▴ 70
0
votes
1
reply
536
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
updated 4 days ago by
aw7
▴ 300 • written 28 days ago by
abhishekghadge
• 0
1
vote
1
reply
163
views
mitochondrial genome assembly pipeline
mammals
mitochondrial-genome
updated 1 day ago by
Ram
43k • written 1 day ago by
m90
▴ 30
0
votes
1
reply
155
views
How can I calculate the OS of each patient?
overall-survival
updated 1 day ago by
ATpoint
82k • written 1 day ago by
Pedro
• 0
1
vote
1
reply
185
views
Help with VG Toolkit: VCF Output is Empty
vg
updated 1 day ago by
Jordan M Eizenga
▴ 460 • written 12 days ago by
sarumonsus
▴ 10
3
votes
1
reply
218
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair
samtools
alignment
updated 4 days ago by
aw7
▴ 300 • written 9 days ago by
Zeng Hao
▴ 40
1
vote
1
reply
172
views
Tool:
Collect dispersed executable files and run them by using bingo.
bingo
updated 1 day ago by
Ram
43k • written 2 days ago by
dwpeng
▴ 10
2
votes
1
reply
264
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
updated 5 days ago by
pjb39
▴ 210 • written 7 days ago by
beantkapoor16
▴ 10
1
vote
1
reply
160
views
API kegg - IndexError: list index out of range
kegg
API
updated 1 day ago by
Nyksubuz
▴ 20 • written 2 days ago by
mirwa.zidi93
• 0
0
votes
1
reply
153
views
Add line under stat test
stats
R
updated 1 day ago by
Nyksubuz
▴ 20 • written 2 days ago by
Ghada
• 0
0
votes
1
reply
151
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
updated 1 day ago by
Nyksubuz
▴ 20 • written 2 days ago by
Luqman
• 0
0
votes
1
reply
234
views
input file in rmats
rmats
updated 6 days ago by
Mathew
▴ 140 • written 8 days ago by
Lambodarswain316
• 0
0
votes
1
reply
227
views
solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* error: could not open input file /geneInfo.tab #2142
STAR
updated 22 hours ago by
GenoMax
142k • written 1 day ago by
huxiangyulove
• 0
0
votes
1
reply
116
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
updated 22 hours ago by
dthorbur
★ 2.0k • written 23 hours ago by
Umer
▴ 50
0
votes
1
reply
157
views
Manual Assembly and Protein Translation, HELP, assignment revision
sequence
university
assembly
protein
genomics
updated 5 days ago by
Philipp Bayer
8.5k • written 5 days ago by
samRayne
• 0
0
votes
1
reply
196
views
Generating .bed file and .map file for polyploid vcf file through plink
bed
polyploid
map
plink
updated 5 days ago by
chrchang523
10k • written 10 days ago by
analyst
▴ 50
4
votes
1
reply
203
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
3 days ago by
J.
▴ 40
0
votes
1
reply
145
views
Post-imputation QC for input into GWAS analyses
gwas
prs
updated 3 days ago by
LauferVA
4.2k • written 3 days ago by
graeme.thorn
▴ 100
1
vote
1
reply
147
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 3 days ago by
Ram
43k • written 3 days ago by
kilcdincer
▴ 10
0
votes
1
reply
244
views
Nomalization - TCGA, RNA-seq and Microarray
TCGA
RNA-seq
Nomalization
Microarray
updated 5 days ago by
Zhenyu Zhang
★ 1.2k • written 8 days ago by
jain72744
▴ 10
0
votes
1
reply
131
views
What is the bin size for Bamcompare?
chip-seq
deeptools
bamcompare
updated 3 days ago by
Ram
43k • written 4 days ago by
Emily
▴ 20
1
vote
1
reply
174
views
The total expressed genes in RNA-Seq data
RNA-SEQ
updated 4 days ago by
ATpoint
82k • written 4 days ago by
Pegasus
▴ 100
0
votes
0
replies
94
views
Help interpreting KEGG module definitions for converting to NetworkX graph
definition
kegg
module
database
genomics
1 day ago by
O.rka
▴ 720
183 results • Page
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Comment: how to treat the replicates while performing WGCNA
by
mavy
▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object
by
Alex Reynolds
35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF)
by
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▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data?
by
Ngrin
• 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
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by
swbarnes2
14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
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by
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4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
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by
hannes.bongartz
• 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
Answer: GG Sankey plot
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bk11
★ 2.5k
You need to change your data table into a 'long' format. You can do something like this- GOs_childs_recursive <- GOs_childs_recursive …
Answer: Trimming tool
by
ntsopoul
▴ 60
I use Trim Galore which automatically recognizes adaptors. https://github.com/FelixKrueger/TrimGalore Here is the script I am using for…
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142k
There are plenty. `bbduk.sh` from BBMap suite (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/ )…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
bk11
★ 2.5k
Please check out [in this link.][1] [1]: https://github.com/jokergoo/ComplexHeatmap/issues/349
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by
dthorbur
★ 2.0k
[Here](https://www.biostars.org/p/9544689/) is a forum post that may answer your question.
Comment: how to treat the replicates while performing WGCNA
by
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3.6k
> 1) I do not want to merge the MEs rather I asked about replicates, as > some replicates of same sample are showing different behavior for…
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For more details about what `samtools quickcheck` actually checks for, add a few `-v`'s to the command line. $ samtools quickcheck -…
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