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116,866 results • Page
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8
votes
6
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12k
views
samtools tview symbols
samtools
updated 36 minutes ago by
Ruqaiya
• 0 • written 8.8 years ago by
biolab
★ 1.4k
1
vote
7
replies
403
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 49 minutes ago by
Pierre Lindenbaum
161k • written 2 days ago by
schmince
• 0
0
votes
3
replies
44
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
56 minutes ago by
SilhouetteQ
• 0
0
votes
1
reply
21
views
Alignment of samples with spike-in
alignment
multimapping
RNA-seq
ChIP-seq
spike-in
updated 1 hour ago by
GenoMax
142k • written 1 hour 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
24
views
How are score_weights calculated in this code?
cell
single
2 hours ago by
carolofharvest
▴ 40
0
votes
0
replies
34
views
How to convert Haps file to vcf file?
pre-phasing
GWAS
imputation
3 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
41
views
Trouble converting tfam and tped to map and ped files
plink
ped
tfam
tped
map
6 hours ago by
Samantha
• 0
0
votes
1
reply
72
views
Microbial Signal Transduction Database
MiST
updated 4 hours ago by
zx8754
11k • written 6 hours ago by
Shravani
• 0
0
votes
0
replies
37
views
input file in rmats
rmats
updated 4 hours ago by
zx8754
11k • written 6 hours ago by
Lambodarswain316
• 0
0
votes
1
reply
80
views
DESeq2 error
DESeq2
updated 6 hours ago by
ATpoint
82k • written 10 hours ago by
sooni
▴ 20
0
votes
0
replies
37
views
Allele specific expression of imprinted gens from 10x scRNA-seq data
scrna-seq
imprinted
10x
genes
8 hours ago by
singcell
• 0
0
votes
1
reply
91
views
When should I use R-MarkDown over R-Script ?
r
rscript
rmarkdown
updated 5 hours ago by
ATpoint
82k • written 8 hours ago by
Amr
▴ 160
0
votes
2
replies
90
views
LncRNA Nomenclature
ENST
nomenclature
lncrna
GBB
ENSG
6 hours ago by
jain72744
▴ 10
0
votes
0
replies
37
views
Nomalization - TCGA, RNA-seq and Microarray
TCGA
RNA-seq
Nomalization
Microarray
8 hours ago by
jain72744
▴ 10
5
votes
2
replies
97
views
EdgeR - relationship between logFC and coefficients
differential-expression
r
edger
updated 8 hours ago by
Gordon Smyth
★ 7.1k • written 10 hours ago by
gBioStar5
▴ 10
2
votes
5
replies
255
views
Importing a fastq file
Fastq
updated 10 hours ago by
size_t
▴ 120 • written 1 day ago by
oumo
• 0
2
votes
1
reply
59
views
Question about methylation location
Methylation
WGBS
bisulfide
updated 1 hour ago by
dthorbur
★ 1.9k • written 13 hours ago by
Eren
• 0
0
votes
0
replies
52
views
Krona Pie-chart taxanomy IDs were not found warning. Taxonomy Classification Metagenomics
Classification
Metagenomics
Krona
Kraken2
13 hours ago by
Aytaç
• 0
0
votes
0
replies
61
views
How do I calculate SE or P value if I only have BETA
prscsx
beta
se
pvalue
updated 4 hours ago by
zx8754
11k • written 15 hours ago by
curious_butterfly
• 0
0
votes
0
replies
58
views
supervised admixture
supervised
admixture
16 hours ago by
RT
▴ 10
0
votes
0
replies
62
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Randomization
Mendelian
two-sample
17 hours ago by
Nikki
• 0
2
votes
0
replies
59
views
News:
course on Landscape Genomics at the EPFL in Lausanne (June 17-21)
LandscapeGenomics
SNPs
LocalAdaptation
GIS
18 hours ago by
carlopecoraro2
★ 2.5k
0
votes
8
replies
299
views
Different output for read length
samtools
BAM
16 hours ago by
marco.barr
▴ 100
0
votes
1
reply
275
views
Snakemake fails to find conda in PBS
snakemake
updated 20 hours ago by
tim.booth
▴ 60 • written 28 days ago by
yixinzeng
• 0
0
votes
2
replies
132
views
Presence of unknown sites in ANNOVAR output file
ANNOVAR
updated 19 hours ago by
GenoMax
142k • written 21 hours ago by
sainavyav22
• 0
2
votes
3
replies
127
views
Truncated metadata file report from ENA Portal API
ena
python
updated 1 hour ago by
GenoMax
142k • written 21 hours ago by
Giulia
• 0
0
votes
0
replies
67
views
What is workflow for de-novo assembling of nuclear and mito genomes of non-model organisms
de-novo
WGS
DNA-seq
assembling
21 hours ago by
Matvii Mykhailichenko
• 0
0
votes
3
replies
471
views
JASPAR2024_getMatrixSet error
JASPAR2024
getMatrixSet
updated 22 hours ago by
Ram
43k • written 11 weeks ago by
maplewj
▴ 10
0
votes
3
replies
152
views
How to convert normalized BigWig file to count matrix?
count-matrix
BigWig
updated 22 hours ago by
Ram
43k • written 1 day ago by
feather-W
• 0
0
votes
3
replies
206
views
bcftools - reducing to "sites-only"?
sites-only
bcftools
updated 23 hours 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
95
views
input file for alternative splicing in rmats in linux
rmats
updated 21 hours ago by
Ram
43k • written 1 day ago by
Lambodarswain316
• 0
0
votes
2
replies
166
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
401
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
2.4k
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
162
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
96
views
What is Deepvariant default filtering values ?
vcf
calling
filter
variant
deepvariant
1 day ago by
Shae
▴ 10
0
votes
1
reply
152
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
118
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
94
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
98
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
216
views
Contig assembly task, errors
genetics
contig
assembly
dna
bioinformatics
updated 11 hours ago by
Philipp Bayer
8.4k • written 1 day ago by
rackbersingh
• 0
1
vote
3
replies
204
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 20 hours ago by
GenoMax
142k • written 1 day ago by
cput
• 0
0
votes
0
replies
104
views
Annotate VCF via VEP for gnomAD annotation considering FILTER column
vep
vcf
gnomad
1 day ago by
asalimih
▴ 60
0
votes
2
replies
223
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 1 day ago by
i.sudbery
19k • written 1 day ago by
Prawesh
• 0
0
votes
9
replies
1.5k
views
kinannote software installation problems
kinannote
updated 1 day ago by
Emanoelle
• 0 • written 5.7 years ago by
Elizabeth
▴ 30
116,866 results • Page
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Recent Votes
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
Comment: Truncated metadata file report from ENA Portal API
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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…
Comment: Alignment of samples with spike-in
by
GenoMax
142k
> but then if you only allow to map uniquely mapped reads, you are losing spike-in information, How so? Spike-in's are generally unique s…
Comment: Truncated metadata file report from ENA Portal API
by
GenoMax
142k
While there is no timeout by default on the `get` operation, you may want to set a higher value and see if that helps, since there is a lar…
Comment: Truncated metadata file report from ENA Portal API
by
Giulia
• 0
The " missing is because of a copy-paste error in the post.. I know wget but my tool is entirely in python. I really don't understand why i…
Comment: UMI-Tools knee-method has great influence on the results of white list
by
Assa Yeroslaviz
★ 1.8k
and if I use the command as such: ``` umi_tools extract --extract-method=regex --error-correct-cell \ --bc-pattern2='(?P…
Comment: UMI-Tools knee-method has great influence on the results of white list
by
i.sudbery
19k
No, UMI-tools won't work this out automatically, you'll need to either switch read1 and read2 or use the new `--read2-only` which is curren…
Comment: Correlation Analysis
by
manaswwm
▴ 510
If your *gene_corr* data frame contains one gene instead of all genes, then the correlation would be per gene. If your *gene_corr* data fra…
Comment: UMI-Tools knee-method has great influence on the results of white list
by
Assa Yeroslaviz
★ 1.8k
I think I might know my problem. The barcodes are in this case on read2 and not on read1. Does umi-tools recognise it automatically, or do …
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