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116,868 results • Page
1 of 2338
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Marker Features variance by cluster, sample, and treatment group
Seurat
scATAC-seq
features
Marker
ArchR
1 hour ago by
naomiboldon
• 0
0
votes
3
replies
55
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk
vcf
converter
liftover
updated 1 hour ago by
Giulio Genovese
▴ 390 • written 2 hours ago by
Omics data mining
▴ 260
8
votes
6
replies
12k
views
samtools tview symbols
samtools
updated 8.8 years ago by
Ashutosh Pandey
12k • written 8.8 years ago by
biolab
★ 1.4k
1
vote
7
replies
438
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 3 hours ago by
Pierre Lindenbaum
161k • written 3 days ago by
schmince
• 0
0
votes
5
replies
107
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
4 minutes ago by
SilhouetteQ
• 0
0
votes
1
reply
44
views
Alignment of samples with spike-in
alignment
multimapping
RNA-seq
ChIP-seq
spike-in
updated 4 hours ago by
GenoMax
142k • written 4 hours ago by
maria.soler
• 0
795
votes
167
replies
143k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.7k • written 7.4 years ago by
Istvan Albert
100k
0
votes
0
replies
38
views
How are score_weights calculated in this code?
cell
single
5 hours ago by
carolofharvest
▴ 40
0
votes
0
replies
46
views
How to convert Haps file to vcf file?
pre-phasing
GWAS
imputation
6 hours ago by
SeoGyun
• 0
2
votes
12
replies
2.7k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 2 days ago by
Anitha
• 0 • written 4.8 years ago by
ww22runner
▴ 60
0
votes
0
replies
48
views
Trouble converting tfam and tped to map and ped files
plink
ped
tfam
tped
map
9 hours ago by
Samantha
• 0
0
votes
1
reply
79
views
Microbial Signal Transduction Database
MiST
updated 7 hours ago by
zx8754
11k • written 9 hours ago by
Shravani
• 0
0
votes
0
replies
45
views
input file in rmats
rmats
updated 7 hours ago by
zx8754
11k • written 9 hours ago by
Lambodarswain316
• 0
0
votes
1
reply
91
views
DESeq2 error
DESeq2
updated 9 hours ago by
ATpoint
82k • written 13 hours ago by
sooni
▴ 20
0
votes
0
replies
45
views
Allele specific expression of imprinted gens from 10x scRNA-seq data
scrna-seq
imprinted
10x
genes
11 hours ago by
singcell
• 0
0
votes
1
reply
102
views
When should I use R-MarkDown over R-Script ?
r
rscript
rmarkdown
updated 8 hours ago by
ATpoint
82k • written 11 hours ago by
Amr
▴ 160
0
votes
2
replies
99
views
LncRNA Nomenclature
ENST
nomenclature
lncrna
GBB
ENSG
9 hours ago by
jain72744
▴ 10
0
votes
0
replies
46
views
Nomalization - TCGA, RNA-seq and Microarray
TCGA
RNA-seq
Nomalization
Microarray
11 hours ago by
jain72744
▴ 10
5
votes
2
replies
104
views
EdgeR - relationship between logFC and coefficients
differential-expression
r
edger
updated 11 hours ago by
Gordon Smyth
★ 7.1k • written 13 hours ago by
gBioStar5
▴ 10
2
votes
5
replies
263
views
Importing a fastq file
Fastq
updated 13 hours ago by
size_t
▴ 120 • written 1 day ago by
oumo
• 0
3
votes
1
reply
82
views
Question about methylation location
Methylation
WGBS
bisulfide
updated 4 hours ago by
dthorbur
★ 1.9k • written 16 hours ago by
Eren
• 0
0
votes
0
replies
58
views
Krona Pie-chart taxanomy IDs were not found warning. Taxonomy Classification Metagenomics
Classification
Metagenomics
Krona
Kraken2
16 hours ago by
Aytaç
• 0
0
votes
0
replies
66
views
How do I calculate SE or P value if I only have BETA
prscsx
beta
se
pvalue
updated 7 hours ago by
zx8754
11k • written 18 hours ago by
curious_butterfly
• 0
0
votes
0
replies
63
views
supervised admixture
supervised
admixture
19 hours ago by
RT
▴ 10
0
votes
0
replies
67
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Randomization
Mendelian
two-sample
20 hours ago by
Nikki
• 0
2
votes
0
replies
67
views
News:
course on Landscape Genomics at the EPFL in Lausanne (June 17-21)
LandscapeGenomics
SNPs
LocalAdaptation
GIS
21 hours ago by
carlopecoraro2
★ 2.5k
0
votes
8
replies
309
views
Different output for read length
samtools
BAM
19 hours ago by
marco.barr
▴ 100
0
votes
1
reply
283
views
Snakemake fails to find conda in PBS
snakemake
updated 23 hours ago by
tim.booth
▴ 60 • written 28 days ago by
yixinzeng
• 0
0
votes
2
replies
137
views
Presence of unknown sites in ANNOVAR output file
ANNOVAR
updated 22 hours ago by
GenoMax
142k • written 1 day ago by
sainavyav22
• 0
2
votes
3
replies
158
views
Truncated metadata file report from ENA Portal API
ena
python
updated 4 hours ago by
GenoMax
142k • written 1 day ago by
Giulia
• 0
0
votes
0
replies
72
views
What is workflow for de-novo assembling of nuclear and mito genomes of non-model organisms
de-novo
WGS
DNA-seq
assembling
1 day ago by
Matvii Mykhailichenko
• 0
0
votes
3
replies
477
views
JASPAR2024_getMatrixSet error
JASPAR2024
getMatrixSet
updated 1 day ago by
Ram
43k • written 11 weeks ago by
maplewj
▴ 10
0
votes
3
replies
159
views
How to convert normalized BigWig file to count matrix?
count-matrix
BigWig
updated 1 day ago by
Ram
43k • written 1 day ago by
feather-W
• 0
0
votes
3
replies
211
views
bcftools - reducing to "sites-only"?
sites-only
bcftools
updated 1 day ago by
Pierre Lindenbaum
161k • written 1 day ago by
Matthew
• 0
3
votes
4
replies
2.9k
views
Have you ever obtained user guide of ExomeCNV?
CNV
updated 4.4 years ago by
lffu_0032
▴ 90 • written 5.2 years ago by
oghzzang
▴ 50
0
votes
1
reply
100
views
input file for alternative splicing in rmats in linux
rmats
updated 1 day ago by
Ram
43k • written 1 day ago by
Lambodarswain316
• 0
0
votes
2
replies
173
views
Server or aws cloud- which one is better for gatk pipeline
aws
server
calling
gatk
cloud
updated 1 day ago by
Michael
54k • written 1 day ago by
ashaneev07
▴ 20
1
vote
1
reply
406
views
ComBat_Seq stuck adjusting the data
Batch-Effect
RNAseq
ComBat-Seq
updated 1 day ago by
Jaïr
• 0 • written 4 months ago by
NorbertK
▴ 10
4
votes
3
replies
2.5k
views
How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when run SamToFastq
samtofasq
picard
validatesamfile
updated 1 day ago by
Pierre Lindenbaum
161k • written 1 day ago by
Lila M
★ 1.2k
2
votes
3
replies
171
views
Nextflow: how to get the process work dir, within the process
nextflow
updated 1 day ago by
Pierre Lindenbaum
161k • written 1 day ago by
ScottDansk
▴ 10
1
vote
0
replies
101
views
What is Deepvariant default filtering values ?
vcf
calling
filter
variant
deepvariant
1 day ago by
Shae
▴ 10
0
votes
1
reply
157
views
Enhanced Volcano-Cut off
foldchange
enhancedvolcano
updated 1 day ago by
marco.barr
▴ 100 • written 1 day ago by
odi
▴ 10
0
votes
6
replies
2.1k
views
Copy number Variation analysis using conumee
R
software error
sequencing
genome
updated 1 day ago by
GenoMax
142k • written 3.2 years ago by
gs000095
▴ 10
1
vote
1
reply
124
views
Conda severely broken after attempting mamba install
biopython
conda
mamba
pycosat
updated 1 day ago by
andres.firrincieli
3.6k • written 1 day ago by
kacollier
▴ 30
1
vote
2
replies
1.6k
views
Seurat CellCycleScoring – confused about the proper order of operations when using SCTransform
CellCycleScoring
SCTransform
Seurat
updated 1 day ago by
Li
• 0 • written 2.3 years ago by
GPM
▴ 10
0
votes
0
replies
99
views
Summary Statistics SNPs not found in Target data
SNP
plink
PRS
updated 1 day ago by
Ram
43k • written 1 day ago by
curious_butterfly
• 0
0
votes
0
replies
104
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair
samtools
alignment
1 day ago by
Zeng Hao
▴ 40
0
votes
3
replies
223
views
Contig assembly task, errors
genetics
contig
assembly
dna
bioinformatics
updated 14 hours ago by
Philipp Bayer
8.4k • written 1 day ago by
rackbersingh
• 0
1
vote
3
replies
212
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 23 hours ago by
GenoMax
142k • written 1 day ago by
cput
• 0
0
votes
0
replies
110
views
Annotate VCF via VEP for gnomAD annotation considering FILTER column
vep
vcf
gnomad
1 day ago by
asalimih
▴ 60
116,868 results • Page
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Comment: Question about methylation location
Comment: Question about methylation location
Comment: Question about methylation location
How to use minimap2?
Comment: RNA seq analysis
Comment: Filtering Multi-sample VCF file for all except one Genotype
Truncated metadata file report from ENA Portal API
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Comment: Too many unpaired forward reads found by Trimmomatic
by
SilhouetteQ
• 0
Using fastp, I found that the adapter sequence for the forward read is corresponding to Trans2_rc in the NexteraPE-PE.fa, while for the re…
Comment: cellranger error message
by
Max
• 0
I think the problem is your fastq_id. This should also read "RabhiN_PHLGEX". Hope this helps!
Comment: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
by
Giulio Genovese
▴ 390
@yokofakun is correct. Also, do notice that the GATK option `--RECOVER_SWAPPED_REF_ALT True` does not work with indels. In general, if your…
Comment: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
by
Pierre Lindenbaum
161k
I think this is useless, in the gatk doc: > For each variant, the tool will look for the target coordinate, reverse-complement and left-al…
Comment: Too many unpaired forward reads found by Trimmomatic
by
GenoMax
142k
Ideally you will know which adapters to use but if you don't then programs like `fastp` can auto-detect them. You could also use `bbduk.sh`…
Comment: UMI-Tools knee-method has great influence on the results of white list
by
i.sudbery
19k
With the `--read2-only` option (which isn't available yet on the bioconda version), this will complain about a lack of `--bc-pattern`. How…
Comment: samtools tview symbols
by
Ruqaiya
• 0
What does the star mean then ?
Comment: RNA seq analysis
by
prifa
▴ 10
it's raw data **fastq.gz**, so for example I have 4 different samples from different tissue, sample A with 3 replicates, samples B,C and D …
Answer: Filtering Multi-sample VCF file for all except one Genotype
by
Pierre Lindenbaum
161k
> The goal is to remove all the variants which are unique to the KWSBambina sample. using jvarkit vcffilterjdk https://jvarkit.readthedo…
Comment: Too many unpaired forward reads found by Trimmomatic
by
SilhouetteQ
• 0
The first example used the adapter file NexteraPE-PE.fa, but it generated more than 50% unpaired data...... The content of NexteraPE-PE.fa…
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
schmince
• 0
Ok so I definitely didn't understand at first what my goal was. The goal is to remove all the variants which are unique to the KWSBambina…
Comment: Question about methylation location
by
dthorbur
★ 1.9k
What data do you have? Generally, you start with sequencing data, which you need to clean and then map to a reference genome. Then dependin…
Comment: Too many unpaired forward reads found by Trimmomatic
by
GenoMax
142k
> when I didn't provide the adapter file Still see the file here `ILLUMINACLIP:./NexteraPE-PE.fa:2:30:10 `, unless that is an empty file.
Comment: Too many unpaired forward reads found by Trimmomatic
by
SilhouetteQ
• 0
Interestingly, when I didn't provide the adapter file, the number of unpaired forward reads was significantly reduced: TrimmomaticPE…
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