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880 results • Page
2 of 18
Sort: Rank
Rank
Views
Votes
Replies
2
votes
3
replies
238
views
error in fun(x((i)), ...) : only defined on a data frame with all numeric alike variables
studio
Cibersort
R
15 hours ago by
Azra
▴ 10
2
votes
1
reply
210
views
Failed to open VCF file
GATK
sentieon
BWA-MEM
updated 2 days ago by
Pierre Lindenbaum
161k • written 2 days ago by
melissachua90
▴ 70
9
votes
7
replies
7.1k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 2 days ago by
Ruqaiya
• 0 • written 5.7 years ago by
xiaozhongzhiping
▴ 20
0
votes
4
replies
352
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
17 hours ago by
beginner123
• 0
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 2 days ago by
Ruqaiya
• 0 • written 6.4 years ago by
dllopezr
▴ 130
0
votes
2
replies
209
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
18 hours ago by
analyst
▴ 50
0
votes
6
replies
375
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
genomics
plink
updated 3 hours ago by
Ram
43k • written 3 days ago by
ajbarrett98
• 0
0
votes
11
replies
475
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
1 day ago by
Tuck898
• 0
3
votes
3
replies
252
views
what is another word for a BLAST "hit"?
blast
alignment
3 days ago by
dec986
▴ 380
0
votes
1
reply
189
views
extract viral protein of interest from 10k whole viral genomes
nBLAST
viral-genome
updated 3 days ago by
Ram
43k • written 3 days ago by
Shwetha
• 0
0
votes
0
replies
157
views
Marker Features variance by cluster, sample, and treatment group
Seurat
scATAC-seq
ArchR
updated 3 days ago by
Ram
43k • written 3 days ago by
naomiboldon
• 0
1
vote
3
replies
263
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk
vcf
liftover
updated 3 days ago by
Ram
43k • written 3 days ago by
Omics data mining
▴ 260
1
vote
7
replies
582
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 3 days ago by
Pierre Lindenbaum
161k • written 6 days ago by
schmince
• 0
0
votes
5
replies
291
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
12 hours ago by
SilhouetteQ
• 0
0
votes
1
reply
176
views
Alignment of samples with spike-in
alignment
multimapping
RNA-seq
ChIP-seq
spike-in
updated 3 days ago by
GenoMax
142k • written 3 days ago by
maria.soler
• 0
0
votes
2
replies
265
views
How are score_weights calculated in this code?
single-cell
2 days ago by
carolofharvest
▴ 40
0
votes
1
reply
208
views
How to convert Haps file to vcf file?
pre-phasing
GWAS
imputation
updated 3 days ago by
curious
▴ 750 • written 3 days ago by
SeoGyun
• 0
0
votes
0
replies
149
views
Trouble converting tfam and tped to map and ped files
plink
ped
tfam
tped
map
3 days ago by
Samantha
• 0
0
votes
1
reply
180
views
Microbial Signal Transduction Database
MiST
updated 3 days ago by
zx8754
11k • written 3 days ago by
Shravani
• 0
0
votes
1
reply
196
views
DESeq2 error
DESeq2
updated 3 days ago by
ATpoint
82k • written 3 days ago by
sooni
▴ 20
0
votes
0
replies
137
views
Allele specific expression of imprinted gens from 10x scRNA-seq data
scrna-seq
imprinted
10x
genes
3 days ago by
singcell
• 0
0
votes
1
reply
203
views
When should I use R-MarkDown over R-Script ?
r
rscript
rmarkdown
updated 3 days ago by
ATpoint
82k • written 3 days ago by
Amr
▴ 160
0
votes
2
replies
214
views
LncRNA Nomenclature
ENST
nomenclature
lncrna
GBB
ENSG
3 days ago by
jain72744
▴ 10
6
votes
2
replies
217
views
EdgeR - relationship between logFC and coefficients
differential-expression
r
edger
updated 3 days ago by
Gordon Smyth
★ 7.1k • written 3 days ago by
gBioStar5
▴ 10
2
votes
5
replies
380
views
Importing a fastq file
Fastq
updated 3 days ago by
size_t
▴ 120 • written 4 days ago by
oumo
• 0
3
votes
1
reply
191
views
Question about methylation location
Methylation
WGBS
bisulfide
updated 3 days ago by
dthorbur
★ 2.0k • written 4 days ago by
Eren
• 0
0
votes
0
replies
147
views
Krona Pie-chart taxanomy IDs were not found warning. Taxonomy Classification Metagenomics
Classification
Metagenomics
Krona
Kraken2
4 days ago by
Aytaç
• 0
0
votes
0
replies
163
views
How do I calculate SE or P value if I only have BETA
prscsx
beta
se
pvalue
updated 3 days ago by
zx8754
11k • written 4 days ago by
curious_butterfly
• 0
0
votes
0
replies
154
views
supervised admixture
supervised
admixture
4 days ago by
RT
▴ 10
2
votes
0
replies
147
views
News:
course on Landscape Genomics at the EPFL in Lausanne (June 17-21)
LandscapeGenomics
SNPs
LocalAdaptation
GIS
4 days ago by
carlopecoraro2
★ 2.5k
0
votes
8
replies
416
views
Different output for read length
samtools
BAM
4 days ago by
marco.barr
▴ 100
0
votes
1
reply
358
views
Snakemake fails to find conda in PBS
snakemake
updated 4 days ago by
tim.booth
▴ 60 • written 4 weeks ago by
yixinzeng
• 0
0
votes
2
replies
213
views
Presence of unknown sites in ANNOVAR output file
ANNOVAR
updated 3 days ago by
Ram
43k • written 4 days ago by
sainavyav22
• 0
3
votes
4
replies
294
views
Truncated metadata file report from ENA Portal API
ena
python
3 days ago by
Giulia
• 0
0
votes
0
replies
180
views
What is workflow for de-novo assembling of nuclear and mito genomes of non-model organisms
de-novo
WGS
DNA-seq
assembling
4 days ago by
Matvii Mykhailichenko
• 0
0
votes
3
replies
547
views
JASPAR2024_getMatrixSet error
JASPAR2024
getMatrixSet
updated 4 days ago by
Ram
43k • written 11 weeks ago by
maplewj
▴ 10
0
votes
5
replies
296
views
How to convert normalized BigWig file to count matrix?
count-matrix
BigWig
22 hours ago by
feather-W
• 0
0
votes
3
replies
283
views
bcftools - reducing to "sites-only"?
sites-only
bcftools
updated 4 days ago by
Pierre Lindenbaum
161k • written 5 days ago by
Matthew
• 0
0
votes
1
reply
144
views
input file for alternative splicing in rmats in linux
rmats
updated 4 days ago by
Ram
43k • written 4 days ago by
Lambodarswain316
• 0
2
votes
2
replies
228
views
Server or aws cloud- which one is better for gatk pipeline
aws
server
calling
gatk
cloud
updated 4 days ago by
Michael
54k • written 4 days ago by
ashaneev07
▴ 20
1
vote
1
reply
441
views
ComBat_Seq stuck adjusting the data
Batch-Effect
RNAseq
ComBat-Seq
updated 4 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 4 days ago by
Pierre Lindenbaum
161k • written 4 days ago by
Lila M
★ 1.2k
2
votes
3
replies
211
views
Nextflow: how to get the process work dir, within the process
nextflow
updated 4 days ago by
Pierre Lindenbaum
161k • written 4 days ago by
ScottDansk
▴ 10
1
vote
0
replies
131
views
What is Deepvariant default filtering values ?
vcf
calling
filter
variant
deepvariant
4 days ago by
Shae
▴ 10
0
votes
1
reply
182
views
Enhanced Volcano-Cut off
foldchange
enhancedvolcano
updated 4 days ago by
marco.barr
▴ 100 • written 5 days ago by
odi
▴ 10
0
votes
6
replies
2.1k
views
Copy number Variation analysis using conumee
R
software error
sequencing
genome
updated 4 days ago by
GenoMax
142k • written 3.2 years ago by
gs000095
▴ 10
1
vote
1
reply
149
views
Conda severely broken after attempting mamba install
biopython
conda
mamba
pycosat
updated 4 days ago by
andres.firrincieli
3.6k • written 4 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 4 days ago by
Li
• 0 • written 2.3 years ago by
GPM
▴ 10
0
votes
0
replies
113
views
Summary Statistics SNPs not found in Target data
SNP
plink
PRS
updated 4 days ago by
Ram
43k • written 4 days ago by
curious_butterfly
• 0
1
vote
4
replies
320
views
Contig assembly task, errors
dna
genetics
contig
assembly
updated 3 hours ago by
Ram
43k • written 5 days ago by
samRayne
• 0
880 results • Page
2 of 18
Recent Votes
Comment: How does gene length effect the number of reads mapped
Comment: How does gene length effect the number of reads mapped
Comment: How does gene length effect the number of reads mapped
Comment: How does gene length effect the number of reads mapped
A: Filtering of VCF, INFO DP or FORMAT DP
What is the difference between GRCh37 and hs37? And hg19?
Answer: Duplicated sequence samtools
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Recent Replies
Comment: Help with IGV abbreviation
by
GeneC
• 0
Thank you for the link and details
Comment: Help with IGV abbreviation
by
GeneC
• 0
Thank you very much for helping with the details.
Comment: How does gene length effect the number of reads mapped
by
Chen
• 0
thank you :)
Answer: Filtering based on alternate allelic balance
by
Arton
• 0
I found the answer when using bcftools. Is there is a way to do this with FilterVcf? bcftools filter --include '(FMT/AD[0:1])/(FMT/A…
Comment: Help with IGV abbreviation
by
GenoMax
142k
Those are SAM format fields. Check section 1.4 here: https://samtools.github.io/hts-specs/SAMv1.pdf > 1:2114:12111:13792 That is part of …
Answer: Help with IGV abbreviation
by
Mathew
▴ 120
Hi, here is a breakdown of each part that you asked about: **flag 99**: This indicates various properties of the read alignment. In this c…
Comment: Kraken2 database
by
Mathew
▴ 120
I don't see any databases with just pathogenic bacteria genomes from just a quick search, I would imagine that using the Standard-16 databa…
Comment: Galaxy StringTie error
by
Mathew
▴ 120
I am not sure if this is true for Galaxy, but when I code in Python, SyntaxWarning: invalid escape sequence '' occurs when you want to add …
Comment: Can diamond prepdb be used to make a taxonomically aware database?
by
GenoMax
142k
Should be possible: https://www.biostars.org/p/430366/ Are you using an older version of `diamond`? Latest versions of `diamond` can use N…
Comment: SNPEff database building error
by
Fungal genetics
• 0
Hi, Below SNPEff database building error I am getting. "FATAL ERROR: Most Exons do not have sequences!" The headers are correct and sam…
Comment: Extracting named fasta sequences according to list with Biopython
by
Rubayetul
• 0
the last line of SeqIO.write(record.....'fasta') in a for loop will input the the last record into new fasta file and it will only contain …
Comment: How to process Bulk WES data?
by
GenoMax
142k
You could use `sarek` (nf-core's exome pipeline) if you don't want to customize or reinvent : https://nf-co.re/sarek/3.4.2
Comment: Empty .best and .sing2 Files After Running Demuxlet
by
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43k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Answer: FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last plac
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11k
Two last seats have just become available. Apply now, if you want them.
Comment: featureCounts output summary assigned value higher than uniquely mapped reads fr
by
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142k
You always need to add the following option when you are using `-p` to count paired-end reads. --countReadPairs If specified, fragm…
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