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751 results • Page
4 of 16
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Votes
Replies
6
votes
4
replies
13k
views
Trimmomatic: What is the difference between paired and unpaired output files in paired-end mode
trimmomatic
paired-end
updated 6 days ago by
Ruqaiya
• 0 • written 6.5 years ago by
dllopezr
▴ 130
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
6
replies
425
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
genomics
plink
updated 4 days ago by
Ram
43k • written 7 days ago by
ajbarrett98
• 0
0
votes
11
replies
545
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
5 days ago by
Tuck898
• 0
3
votes
3
replies
284
views
what is another word for a BLAST "hit"?
blast
alignment
7 days ago by
dec986
▴ 380
0
votes
1
reply
205
views
extract viral protein of interest from 10k whole viral genomes
nBLAST
viral-genome
updated 7 days ago by
Ram
43k • written 7 days ago by
Shwetha
• 0
0
votes
0
replies
165
views
Marker Features variance by cluster, sample, and treatment group
Seurat
scATAC-seq
ArchR
updated 7 days ago by
Ram
43k • written 7 days ago by
naomiboldon
• 0
1
vote
3
replies
287
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk
vcf
liftover
updated 7 days ago by
Ram
43k • written 7 days ago by
Omics data mining
▴ 260
2
votes
9
replies
706
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 3 days ago by
Pierre Lindenbaum
161k • written 10 days ago by
schmince
• 0
0
votes
5
replies
319
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
4 days ago by
SilhouetteQ
• 0
0
votes
1
reply
192
views
Alignment of samples with spike-in
alignment
multimapping
RNA-seq
ChIP-seq
spike-in
updated 7 days ago by
GenoMax
142k • written 7 days ago by
maria.soler
• 0
0
votes
2
replies
297
views
How are score_weights calculated in this code?
single-cell
7 days ago by
carolofharvest
▴ 40
0
votes
1
reply
225
views
How to convert Haps file to vcf file?
pre-phasing
GWAS
imputation
updated 7 days ago by
curious
▴ 750 • written 8 days ago by
SeoGyun
• 0
0
votes
0
replies
157
views
Trouble converting tfam and tped to map and ped files
plink
ped
tfam
tped
map
8 days ago by
Samantha
• 0
0
votes
1
reply
192
views
Microbial Signal Transduction Database
MiST
updated 8 days ago by
zx8754
11k • written 8 days ago by
Shravani
• 0
1
vote
1
reply
220
views
DESeq2 error
DESeq2
updated 8 days ago by
ATpoint
82k • written 8 days ago by
sooni
▴ 20
0
votes
0
replies
145
views
Allele specific expression of imprinted gens from 10x scRNA-seq data
scrna-seq
imprinted
10x
genes
8 days ago by
singcell
• 0
0
votes
1
reply
219
views
When should I use R-MarkDown over R-Script ?
r
rscript
rmarkdown
updated 8 days ago by
ATpoint
82k • written 8 days ago by
Amr
▴ 160
0
votes
2
replies
232
views
LncRNA Nomenclature
ENST
nomenclature
lncrna
GBB
ENSG
8 days ago by
jain72744
▴ 10
6
votes
2
replies
243
views
EdgeR - relationship between logFC and coefficients
differential-expression
r
edger
updated 8 days ago by
Gordon Smyth
★ 7.2k • written 8 days ago by
gBioStar5
▴ 10
2
votes
5
replies
412
views
Importing a fastq file
Fastq
updated 8 days ago by
size_t
▴ 120 • written 9 days ago by
oumo
• 0
3
votes
1
reply
207
views
Question about methylation location
Methylation
WGBS
bisulfide
updated 7 days ago by
dthorbur
★ 2.0k • written 8 days ago by
Eren
• 0
0
votes
0
replies
157
views
Krona Pie-chart taxanomy IDs were not found warning. Taxonomy Classification Metagenomics
Classification
Metagenomics
Krona
Kraken2
8 days ago by
Aytaç
• 0
0
votes
0
replies
171
views
How do I calculate SE or P value if I only have BETA
prscsx
beta
se
pvalue
updated 8 days ago by
zx8754
11k • written 8 days ago by
curious_butterfly
• 0
0
votes
0
replies
164
views
supervised admixture
supervised
admixture
8 days ago by
RT
▴ 10
2
votes
0
replies
157
views
News:
course on Landscape Genomics at the EPFL in Lausanne (June 17-21)
LandscapeGenomics
SNPs
LocalAdaptation
GIS
8 days ago by
carlopecoraro2
★ 2.5k
0
votes
8
replies
461
views
Different output for read length
samtools
BAM
8 days ago by
marco.barr
▴ 130
0
votes
1
reply
368
views
Snakemake fails to find conda in PBS
snakemake
updated 8 days ago by
tim.booth
▴ 60 • written 5 weeks ago by
yixinzeng
• 0
0
votes
2
replies
230
views
Presence of unknown sites in ANNOVAR output file
ANNOVAR
updated 7 days ago by
Ram
43k • written 8 days ago by
sainavyav22
• 0
3
votes
4
replies
322
views
Truncated metadata file report from ENA Portal API
ena
python
7 days ago by
Giulia
• 0
0
votes
0
replies
189
views
What is workflow for de-novo assembling of nuclear and mito genomes of non-model organisms
de-novo
WGS
DNA-seq
assembling
8 days ago by
Matvii Mykhailichenko
• 0
0
votes
3
replies
564
views
JASPAR2024_getMatrixSet error
JASPAR2024
getMatrixSet
updated 8 days ago by
Ram
43k • written 12 weeks ago by
maplewj
▴ 10
0
votes
5
replies
335
views
How to convert normalized BigWig file to count matrix?
count-matrix
BigWig
5 days ago by
feather-W
• 0
0
votes
3
replies
305
views
bcftools - reducing to "sites-only"?
sites-only
bcftools
updated 8 days ago by
Pierre Lindenbaum
161k • written 9 days ago by
Matthew
• 0
0
votes
1
reply
156
views
input file for alternative splicing in rmats in linux
rmats
updated 8 days ago by
Ram
43k • written 8 days ago by
Lambodarswain316
• 0
2
votes
2
replies
251
views
Server or aws cloud- which one is better for gatk pipeline
aws
server
calling
gatk
cloud
updated 8 days ago by
Michael
54k • written 9 days ago by
ashaneev07
▴ 20
1
vote
1
reply
455
views
ComBat_Seq stuck adjusting the data
Batch-Effect
RNAseq
ComBat-Seq
updated 8 days ago by
Jaïr
• 0 • written 4 months ago by
NorbertK
▴ 10
4
votes
3
replies
2.9k
views
How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when run SamToFastq
samtofasq
picard
validatesamfile
updated 8 days ago by
Pierre Lindenbaum
161k • written 9 days ago by
Lila M
★ 1.2k
2
votes
3
replies
234
views
Nextflow: how to get the process work dir, within the process
nextflow
updated 8 days ago by
Pierre Lindenbaum
161k • written 9 days ago by
ScottDansk
▴ 10
1
vote
0
replies
143
views
What is Deepvariant default filtering values ?
vcf
calling
filter
variant
deepvariant
9 days ago by
Shae
▴ 10
0
votes
1
reply
195
views
Enhanced Volcano-Cut off
foldchange
enhancedvolcano
updated 9 days ago by
marco.barr
▴ 130 • written 9 days ago by
odi
▴ 10
0
votes
6
replies
2.1k
views
Copy number Variation analysis using conumee
R
software error
sequencing
genome
updated 8 days ago by
GenoMax
142k • written 3.2 years ago by
gs000095
▴ 10
1
vote
1
reply
162
views
Conda severely broken after attempting mamba install
biopython
conda
mamba
pycosat
updated 9 days ago by
andres.firrincieli
3.6k • written 9 days ago by
kacollier
▴ 30
1
vote
2
replies
1.7k
views
Seurat CellCycleScoring – confused about the proper order of operations when using SCTransform
CellCycleScoring
SCTransform
Seurat
updated 9 days ago by
Li
• 0 • written 2.3 years ago by
GPM
▴ 10
0
votes
0
replies
119
views
Summary Statistics SNPs not found in Target data
SNP
plink
PRS
updated 9 days ago by
Ram
43k • written 9 days ago by
curious_butterfly
• 0
1
vote
4
replies
342
views
Contig assembly task, errors
dna
genetics
contig
assembly
updated 4 days ago by
Ram
43k • written 9 days ago by
samRayne
• 0
1
vote
3
replies
269
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 8 days ago by
GenoMax
142k • written 9 days ago by
cput
• 0
0
votes
0
replies
122
views
Annotate VCF via VEP for gnomAD annotation considering FILTER column
vep
vcf
gnomad
9 days ago by
asalimih
▴ 60
0
votes
9
replies
1.5k
views
kinannote software installation problems
kinannote
updated 9 days ago by
Emanoelle
• 0 • written 5.8 years ago by
Elizabeth
▴ 30
0
votes
2
replies
233
views
Obtaining Infinium Methylation450K manifest for hg38
TCGA
hg38
methylation
Illumina
updated 5 days ago by
Zhenyu Zhang
★ 1.2k • written 9 days ago by
elisheva
▴ 120
751 results • Page
4 of 16
Recent Votes
Answer: ChatGPT optimized for bioinformatics questions
Comment: ChatGPT optimized for bioinformatics questions
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C: How can I perform Differential expression analysis with just one control and one
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Recent Replies
Answer: RNAseq coverage vs depth for transcript isoform expression?
by
Gordon Smyth
★ 7.2k
See the exploration of isoform precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167. Our resul…
Comment: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
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
aidangcruickshank
▴ 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.
Answer: Design for complex RNA-Seq experiment using Deseq2
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…
Comment: GG Sankey plot
by
LauferVA
4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
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
by
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…
Answer: Trimming tool
by
GenoMax
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
Comment: Reconstruction of locus, order contigs
by
dthorbur
★ 2.0k
[Here](https://www.biostars.org/p/9544689/) is a forum post that may answer your question.
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