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116,871 results • Page
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extract viral protein of interest from 10k whole viral genomes
large
viral
nBLAST
datasets
genome
updated 50 minutes ago by
GenoMax
142k • written 1 hour ago by
Shwetha
• 0
0
votes
0
replies
25
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
2 hours ago by
beantkapoor16
• 0
0
votes
9
replies
154
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
1 hour ago by
Tuck898
• 0
0
votes
0
replies
44
views
Marker Features variance by cluster, sample, and treatment group
Seurat
scATAC-seq
features
Marker
ArchR
5 hours ago by
naomiboldon
• 0
1
vote
3
replies
114
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk
vcf
converter
liftover
updated 5 hours ago by
Giulio Genovese
▴ 400 • written 6 hours ago by
Omics data mining
▴ 260
9
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
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
1
vote
7
replies
455
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 8 hours ago by
Pierre Lindenbaum
161k • written 3 days ago by
schmince
• 0
0
votes
5
replies
160
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
4 hours ago by
SilhouetteQ
• 0
0
votes
1
reply
61
views
Alignment of samples with spike-in
alignment
multimapping
RNA-seq
ChIP-seq
spike-in
updated 8 hours ago by
GenoMax
142k • written 8 hours ago by
maria.soler
• 0
0
votes
0
replies
55
views
How are score_weights calculated in this code?
cell
single
9 hours ago by
carolofharvest
▴ 40
0
votes
1
reply
66
views
How to convert Haps file to vcf file?
pre-phasing
GWAS
imputation
updated 1 hour ago by
curious
▴ 750 • written 11 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
55
views
Trouble converting tfam and tped to map and ped files
plink
ped
tfam
tped
map
13 hours ago by
Samantha
• 0
0
votes
1
reply
86
views
Microbial Signal Transduction Database
MiST
updated 11 hours ago by
zx8754
11k • written 13 hours ago by
Shravani
• 0
0
votes
0
replies
51
views
input file in rmats
rmats
updated 11 hours ago by
zx8754
11k • written 14 hours ago by
Lambodarswain316
• 0
0
votes
1
reply
97
views
DESeq2 error
DESeq2
updated 14 hours ago by
ATpoint
82k • written 17 hours ago by
sooni
▴ 20
0
votes
0
replies
51
views
Allele specific expression of imprinted gens from 10x scRNA-seq data
scrna-seq
imprinted
10x
genes
15 hours ago by
singcell
• 0
0
votes
1
reply
109
views
When should I use R-MarkDown over R-Script ?
r
rscript
rmarkdown
updated 12 hours ago by
ATpoint
82k • written 15 hours ago by
Amr
▴ 160
0
votes
2
replies
106
views
LncRNA Nomenclature
ENST
nomenclature
lncrna
GBB
ENSG
13 hours ago by
jain72744
▴ 10
0
votes
0
replies
52
views
Nomalization - TCGA, RNA-seq and Microarray
TCGA
RNA-seq
Nomalization
Microarray
15 hours ago by
jain72744
▴ 10
6
votes
2
replies
115
views
EdgeR - relationship between logFC and coefficients
differential-expression
r
edger
updated 15 hours ago by
Gordon Smyth
★ 7.1k • written 17 hours ago by
gBioStar5
▴ 10
2
votes
5
replies
272
views
Importing a fastq file
Fastq
updated 17 hours ago by
size_t
▴ 120 • written 1 day ago by
oumo
• 0
3
votes
1
reply
95
views
Question about methylation location
Methylation
WGBS
bisulfide
updated 8 hours ago by
dthorbur
★ 1.9k • written 20 hours ago by
Eren
• 0
0
votes
0
replies
63
views
Krona Pie-chart taxanomy IDs were not found warning. Taxonomy Classification Metagenomics
Classification
Metagenomics
Krona
Kraken2
21 hours ago by
Aytaç
• 0
0
votes
0
replies
71
views
How do I calculate SE or P value if I only have BETA
prscsx
beta
se
pvalue
updated 11 hours ago by
zx8754
11k • written 22 hours ago by
curious_butterfly
• 0
0
votes
0
replies
68
views
supervised admixture
supervised
admixture
23 hours ago by
RT
▴ 10
0
votes
0
replies
72
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Randomization
Mendelian
two-sample
1 day ago by
Nikki
• 0
2
votes
0
replies
72
views
News:
course on Landscape Genomics at the EPFL in Lausanne (June 17-21)
LandscapeGenomics
SNPs
LocalAdaptation
GIS
1 day ago by
carlopecoraro2
★ 2.5k
0
votes
8
replies
316
views
Different output for read length
samtools
BAM
1 day ago by
marco.barr
▴ 100
0
votes
1
reply
288
views
Snakemake fails to find conda in PBS
snakemake
updated 1 day ago by
tim.booth
▴ 60 • written 28 days ago by
yixinzeng
• 0
0
votes
2
replies
141
views
Presence of unknown sites in ANNOVAR output file
ANNOVAR
updated 1 day ago by
GenoMax
142k • written 1 day ago by
sainavyav22
• 0
3
votes
4
replies
183
views
Truncated metadata file report from ENA Portal API
ena
python
58 minutes ago by
Giulia
• 0
0
votes
0
replies
76
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
483
views
JASPAR2024_getMatrixSet error
JASPAR2024
getMatrixSet
updated 1 day ago by
Ram
43k • written 11 weeks ago by
maplewj
▴ 10
0
votes
3
replies
163
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
216
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
104
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
1
vote
2
replies
183
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
410
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
2.8k
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
177
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
106
views
What is Deepvariant default filtering values ?
vcf
calling
filter
variant
deepvariant
1 day ago by
Shae
▴ 10
0
votes
1
reply
161
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
129
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
104
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
109
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair
samtools
alignment
1 day ago by
Zeng Hao
▴ 40
116,871 results • Page
1 of 2338
Recent Votes
Comment: Where to get the following bed file?
Comment: Truncated metadata file report from ENA Portal API
Comment: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
C: PLINK --score Erroe
Answer: PLINK Error: No valid entries in --score file.
C: PLINK Error: No valid entries in --score file.
Comment: Can I readmap short reads to rDNA references?
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Recent Replies
Comment: Can I readmap short reads to rDNA references?
by
GenoMax
142k
If these are short reads and the organisms are related then you are going to have a difficult time classifying the reads.
Comment: extract viral protein of interest from 10k whole viral genomes
by
GenoMax
142k
With a large dataset it is always best to do the search locally (or in the cloud, if you don't have necessary hardware available locally).
Comment: Truncated metadata file report from ENA Portal API
by
Giulia
• 0
Thank you so much for your hint! I'll look into this!
Comment: How to convert Haps file to vcf file?
by
curious
▴ 750
unzip haps then: bin/shapeit \ -convert \ --input-haps {haps_prefix} \ --thread {cpus} \ --output-…
Comment: Can I readmap short reads to rDNA references?
by
aniigodwinn
• 0
Still on this, the reads are from org a, org b, and environmental contaminants. I have a fairly good idea what org b might be but i need to…
Comment: fastq screen aligner no specified.
by
Ximena
• 0
Thank u so much, my OS is linux. I will try your advice.
Comment: In IGV is this a heterogeneous mutation or false call?
by
Tuck898
• 0
No worries, I can completely appreciate that. I am having investigations similar to a condition causes by the RYR2 gene and was wondering i…
Comment: In IGV is this a heterogeneous mutation or false call?
by
Pierre Lindenbaum
161k
> RYR1 underneath although I was originally looking at the RYR2 gene. Sorry to sound stupid but does this make sense to what I've previousl…
Comment: In IGV is this a heterogeneous mutation or false call?
by
Tuck898
• 0
When click the blat it brings me to chr19 and mentions the RYR1 underneath although I was originally looking at the RYR2 gene. Sorry to sou…
Comment: In IGV is this a heterogeneous mutation or false call?
by
Tuck898
• 0
Thanks for that! I'll try and have a look and see what is amiss if I can... In your opinion what do you feel is wrong in my alignment from…
Comment: In IGV is this a heterogeneous mutation or false call?
by
Pierre Lindenbaum
161k
yeah.. look at that, there is something wrong in your alignment, many reads were mapped in a location but they are all clipped, so somethin…
Comment: Custom Reference panel creation for data imputation from .vcf files
by
analyst
▴ 50
Hi [Kevin][1]! I have 80 samples of GBS data. I have called variants through GATK pipeline. Now I have to perform imputation. Do I need …
Comment: In IGV is this a heterogeneous mutation or false call?
by
Tuck898
• 0
Ah I've just found 'show soft clipped bases' and this is what comes up... how come it is all greyed out? ![enter image description here][…
Comment: In IGV is this a heterogeneous mutation or false call?
by
Tuck898
• 0
I've just displayed clipped bases and this is what it shows. Does this look right? ![enter image description here][1] ![enter imag…
Comment: In IGV is this a heterogeneous mutation or false call?
by
Tuck898
• 0
Hi, I really appreciate you taking the time to reply. I'm still learning with IGV and sorry to sound very inexperienced but how would I che…
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