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916 results • Page
1 of 19
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0
votes
0
replies
8
views
imputation through beagle
panel
beagle
reference
imputation
20 minutes ago by
analyst
▴ 50
0
votes
0
replies
10
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
45 minutes ago by
analyst
▴ 50
0
votes
0
replies
25
views
Failed to open VCF file
GATK
sentieon
BWA-MEM
2 hours ago by
melissachua90
▴ 70
0
votes
0
replies
48
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
7 hours ago by
Christopher
• 0
0
votes
1
reply
80
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
plink
bioinformatics
genomics
updated 10 hours ago by
Pierre Lindenbaum
161k • written 11 hours ago by
ajbarrett98
• 0
0
votes
10
replies
296
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
updated 11 hours ago by
swbarnes2
14k • written 18 hours ago by
Tuck898
• 0
1
vote
3
replies
117
views
Tassel 5 GBS: Is there something wrong with my fastqs?
tassel
fastq
gbs
updated 11 hours ago by
GenoMax
142k • written 12 hours ago by
meck
• 0
3
votes
3
replies
123
views
what is another word for a BLAST "hit"?
blast
alignment
12 hours ago by
dec986
▴ 380
1
vote
2
replies
90
views
Genome Assembly task + Protein Translation, assignment advice on a question
sequence-analysis
protein-synthesis
just now by
rackbersingh
• 0
0
votes
1
reply
98
views
extract viral protein of interest from 10k whole viral genomes
nBLAST
viral-genome
updated 13 hours ago by
Ram
43k • written 15 hours ago by
Shwetha
• 0
0
votes
0
replies
65
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
16 hours ago by
beantkapoor16
• 0
0
votes
0
replies
67
views
Marker Features variance by cluster, sample, and treatment group
Seurat
scATAC-seq
ArchR
updated 13 hours ago by
Ram
43k • written 19 hours ago by
naomiboldon
• 0
1
vote
3
replies
163
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk
vcf
liftover
updated 13 hours ago by
Ram
43k • written 20 hours ago by
Omics data mining
▴ 260
1
vote
7
replies
479
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 21 hours ago by
Pierre Lindenbaum
161k • written 3 days ago by
schmince
• 0
0
votes
5
replies
189
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
18 hours ago by
SilhouetteQ
• 0
0
votes
1
reply
91
views
Alignment of samples with spike-in
alignment
multimapping
RNA-seq
ChIP-seq
spike-in
updated 22 hours ago by
GenoMax
142k • written 22 hours ago by
maria.soler
• 0
0
votes
2
replies
125
views
How are score_weights calculated in this code?
single-cell
40 minutes ago by
carolofharvest
▴ 40
0
votes
1
reply
125
views
How to convert Haps file to vcf file?
pre-phasing
GWAS
imputation
updated 14 hours ago by
curious
▴ 750 • written 1 day ago by
SeoGyun
• 0
2
votes
12
replies
2.7k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 3 days ago by
Anitha
• 0 • written 4.8 years ago by
ww22runner
▴ 60
0
votes
0
replies
76
views
Trouble converting tfam and tped to map and ped files
plink
ped
tfam
tped
map
1 day ago by
Samantha
• 0
0
votes
1
reply
109
views
Microbial Signal Transduction Database
MiST
updated 1 day ago by
zx8754
11k • written 1 day ago by
Shravani
• 0
0
votes
0
replies
71
views
input file in rmats
rmats
updated 1 day ago by
zx8754
11k • written 1 day ago by
Lambodarswain316
• 0
0
votes
1
reply
119
views
DESeq2 error
DESeq2
updated 1 day ago by
ATpoint
82k • written 1 day ago by
sooni
▴ 20
0
votes
0
replies
70
views
Allele specific expression of imprinted gens from 10x scRNA-seq data
scrna-seq
imprinted
10x
genes
1 day ago by
singcell
• 0
0
votes
1
reply
130
views
When should I use R-MarkDown over R-Script ?
r
rscript
rmarkdown
updated 1 day ago by
ATpoint
82k • written 1 day ago by
Amr
▴ 160
0
votes
2
replies
126
views
LncRNA Nomenclature
ENST
nomenclature
lncrna
GBB
ENSG
1 day ago by
jain72744
▴ 10
0
votes
0
replies
73
views
Nomalization - TCGA, RNA-seq and Microarray
TCGA
RNA-seq
Nomalization
Microarray
1 day ago by
jain72744
▴ 10
6
votes
2
replies
137
views
EdgeR - relationship between logFC and coefficients
differential-expression
r
edger
updated 1 day ago by
Gordon Smyth
★ 7.1k • written 1 day ago by
gBioStar5
▴ 10
2
votes
5
replies
294
views
Importing a fastq file
Fastq
updated 1 day ago by
size_t
▴ 120 • written 2 days ago by
oumo
• 0
3
votes
1
reply
116
views
Question about methylation location
Methylation
WGBS
bisulfide
updated 22 hours ago by
dthorbur
★ 1.9k • written 1 day ago by
Eren
• 0
0
votes
0
replies
81
views
Krona Pie-chart taxanomy IDs were not found warning. Taxonomy Classification Metagenomics
Classification
Metagenomics
Krona
Kraken2
1 day ago by
Aytaç
• 0
0
votes
0
replies
93
views
How do I calculate SE or P value if I only have BETA
prscsx
beta
se
pvalue
updated 1 day ago by
zx8754
11k • written 1 day ago by
curious_butterfly
• 0
0
votes
0
replies
87
views
supervised admixture
supervised
admixture
1 day ago by
RT
▴ 10
0
votes
0
replies
91
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
90
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
335
views
Different output for read length
samtools
BAM
1 day ago by
marco.barr
▴ 100
0
votes
1
reply
305
views
Snakemake fails to find conda in PBS
snakemake
updated 1 day ago by
tim.booth
▴ 60 • written 29 days ago by
yixinzeng
• 0
0
votes
2
replies
165
views
Presence of unknown sites in ANNOVAR output file
ANNOVAR
updated 13 hours ago by
Ram
43k • written 1 day ago by
sainavyav22
• 0
3
votes
4
replies
239
views
Truncated metadata file report from ENA Portal API
ena
python
14 hours ago by
Giulia
• 0
0
votes
0
replies
108
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
506
views
JASPAR2024_getMatrixSet error
JASPAR2024
getMatrixSet
updated 1 day ago by
Ram
43k • written 11 weeks ago by
maplewj
▴ 10
0
votes
3
replies
187
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
240
views
bcftools - reducing to "sites-only"?
sites-only
bcftools
updated 1 day ago by
Pierre Lindenbaum
161k • written 2 days ago by
Matthew
• 0
0
votes
1
reply
123
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
201
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 2 days ago by
ashaneev07
▴ 20
1
vote
1
reply
428
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
2.9k
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 2 days ago by
Lila M
★ 1.2k
2
votes
3
replies
198
views
Nextflow: how to get the process work dir, within the process
nextflow
updated 1 day ago by
Pierre Lindenbaum
161k • written 2 days ago by
ScottDansk
▴ 10
1
vote
0
replies
127
views
What is Deepvariant default filtering values ?
vcf
calling
filter
variant
deepvariant
2 days ago by
Shae
▴ 10
0
votes
1
reply
176
views
Enhanced Volcano-Cut off
foldchange
enhancedvolcano
updated 2 days ago by
marco.barr
▴ 100 • written 2 days ago by
odi
▴ 10
916 results • Page
1 of 19
Recent Votes
Answer: Tissue-specific DEG analysis with DEseq2
Comment: Tassel 5 GBS: Is there something wrong with my fastqs?
Answer: what is another word for a BLAST "hit"?
Comment: what is another word for a BLAST "hit"?
Comment: what is another word for a BLAST "hit"?
Comment: How can I merge GFF files together to produce a file with gene functions from bo
Comment: Contig assembly task, errors
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All
Popular Question
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melissachua90
▴ 70
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octpus616
▴ 100
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to
turcoa1
• 0
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to
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10k
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Lélé
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dthorbur
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maria.soler
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Recent Replies
Comment: How are score_weights calculated in this code?
by
carolofharvest
▴ 40
I've found this code [in this site :][1] . It doesn't seem like they've shared any additional information about this in the previous line…
Comment: Correlation Analysis
by
Researcher
▴ 30
Thank you so much. I ran based on the above code and found that all gene columns have the same values, which you obtain as the average corr…
Answer: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
Pierre Lindenbaum
161k
use bcftools merge with --force-samples and then use jvarkit https://jvarkit.readthedocs.io/en/latest/VcfFilterJdk/ to replace the no-call …
Answer: In IGV is this a heterogeneous mutation or false call?
by
swbarnes2
14k
Since all the reads that show the alternate allele have to be clipped to align there, I'd say those reads are misaligned. I would say that…
Comment: Tassel 5 GBS: Is there something wrong with my fastqs?
by
GenoMax
142k
> Here's a few lines from the head of the raw fastq If your files are actually compressed (as their names suggest) then you should not be …
Comment: Tassel 5 GBS: Is there something wrong with my fastqs?
by
GenoMax
142k
If you added the `\` before the `+` then there is no need for it. It makes it appear that the sequences are not in proper fastq format. Ple…
Comment: Tassel 5 GBS: Is there something wrong with my fastqs?
by
Mensur Dlakic
★ 27k
This seems to be the same unanswered question as before, except that its description is split over two threads. You are now forcing us to r…
Answer: what is another word for a BLAST "hit"?
by
dec986
▴ 380
I'll probably go with "matches" even though it doesn't sound as good as just "hit"
Comment: what is another word for a BLAST "hit"?
by
bk11
★ 2.4k
> hits from BLAST hits sequences
Comment: what is another word for a BLAST "hit"?
by
Pierre Lindenbaum
161k
> is there a synonym for hits from BLAST? alignment
Comment: How are score_weights calculated in this code?
by
Ram
43k
Is this ALL the context you can give us?
Comment: Genome Assembly task + Protein Translation, assignment advice on a question
by
Ram
43k
Where did you copy-paste this from? It looks like an assignment question.
Comment: Contig assembly task, errors
by
rackbersingh
• 0
Hi Phillip, Thanks for sharing you knowledge and funnily enough this really was an amplitude test, but anyways your sharing of knowledge h…
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).
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