Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : this week
all time
today
this week
this month
this year
185 results • Page
1 of 4
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
10
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
eigencorplot
PCAtools
deseq2
pca
41 minutes ago by
BioinfGuru
★ 1.7k
0
votes
1
reply
32
views
Output file of satools flagstat empty
samtools-flagstat
updated 4 minutes ago by
GenoMax
142k • written 1 hour ago by
ramendra.sarma
• 0
2
votes
8
replies
114
views
joint callset and vcf sorting, unknown TAG issue
sort
bcftools
GLNexus
merge
VCF
updated 2 minutes ago by
Pierre Lindenbaum
161k • written 3 hours ago by
Matteo Ungaro
▴ 100
0
votes
0
replies
44
views
News:
Online course: An Introduction to Nanopore Direct RNA Sequencing
Nanopore
RNAseq
7 hours ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
144
views
input file in rmats
rmats
updated 8 hours ago by
Mathew
▴ 90 • written 2 days ago by
Lambodarswain316
• 0
0
votes
1
reply
157
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
updated 16 hours ago by
Mathew
▴ 90 • written 1 day ago by
Christopher
• 0
6
votes
6
replies
202
views
Longest transcript variant per gene
transcript
longest
variant
orthofinder
updated 10 hours ago by
Mathew
▴ 90 • written 16 hours ago by
sansan_96
▴ 90
2
votes
2
replies
142
views
error in fun(x((i)), ...) : only defined on a data frame with all numeric alike variables
studio
Cibersort
R
updated 17 hours ago by
Mathew
▴ 90 • written 19 hours ago by
Azra
▴ 10
2
votes
1
reply
150
views
Failed to open VCF file
GATK
sentieon
BWA-MEM
updated 1 day ago by
Pierre Lindenbaum
161k • written 1 day ago by
melissachua90
▴ 70
9
votes
7
replies
7.1k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 1 day ago by
Ruqaiya
• 0 • written 5.7 years ago by
xiaozhongzhiping
▴ 20
0
votes
2
replies
183
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
2 hours ago by
beginner123
• 0
6
votes
4
replies
12k
views
Trimmomatic: What is the difference between paired and unpaired output files in paired-end mode
trimmomatic
paired-end
updated 1 day ago by
Ruqaiya
• 0 • written 6.4 years ago by
dllopezr
▴ 130
0
votes
0
replies
78
views
imputation through beagle
panel
beagle
reference
imputation
1 day ago by
analyst
▴ 50
0
votes
1
reply
120
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
updated 1 day ago by
Pierre Lindenbaum
161k • written 1 day ago by
analyst
▴ 50
0
votes
4
replies
249
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
plink
bioinformatics
genomics
18 hours ago by
ajbarrett98
• 0
0
votes
10
replies
360
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
updated 1 day ago by
swbarnes2
14k • written 1 day ago by
Tuck898
• 0
1
vote
3
replies
181
views
Tassel 5 GBS: Is there something wrong with my fastqs?
tassel
fastq
gbs
updated 1 day ago by
GenoMax
142k • written 1 day ago by
meck
• 0
3
votes
3
replies
191
views
what is another word for a BLAST "hit"?
blast
alignment
1 day ago by
dec986
▴ 380
1
vote
2
replies
184
views
Genome Assembly task + Protein Translation, assignment advice on a question
sequence-analysis
protein-synthesis
1 day ago by
rackbersingh
• 0
0
votes
1
reply
139
views
extract viral protein of interest from 10k whole viral genomes
nBLAST
viral-genome
updated 1 day ago by
Ram
43k • written 1 day ago by
Shwetha
• 0
0
votes
0
replies
106
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
1 day ago by
beantkapoor16
• 0
0
votes
0
replies
108
views
Marker Features variance by cluster, sample, and treatment group
Seurat
scATAC-seq
ArchR
updated 1 day ago by
Ram
43k • written 1 day ago by
naomiboldon
• 0
1
vote
3
replies
209
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk
vcf
liftover
updated 1 day ago by
Ram
43k • written 2 days ago by
Omics data mining
▴ 260
1
vote
7
replies
521
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 2 days ago by
Pierre Lindenbaum
161k • written 4 days ago by
schmince
• 0
0
votes
5
replies
241
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
1 day ago by
SilhouetteQ
• 0
0
votes
1
reply
131
views
Alignment of samples with spike-in
alignment
multimapping
RNA-seq
ChIP-seq
spike-in
updated 2 days ago by
GenoMax
142k • written 2 days ago by
maria.soler
• 0
0
votes
2
replies
218
views
How are score_weights calculated in this code?
single-cell
1 day ago by
carolofharvest
▴ 40
0
votes
1
reply
169
views
How to convert Haps file to vcf file?
pre-phasing
GWAS
imputation
updated 1 day ago by
curious
▴ 750 • written 2 days ago by
SeoGyun
• 0
2
votes
12
replies
2.7k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 4 days ago by
Anitha
• 0 • written 4.8 years ago by
ww22runner
▴ 60
0
votes
0
replies
112
views
Trouble converting tfam and tped to map and ped files
plink
ped
tfam
tped
map
2 days ago by
Samantha
• 0
0
votes
1
reply
144
views
Microbial Signal Transduction Database
MiST
updated 2 days ago by
zx8754
11k • written 2 days ago by
Shravani
• 0
0
votes
1
reply
156
views
DESeq2 error
DESeq2
updated 2 days ago by
ATpoint
82k • written 2 days ago by
sooni
▴ 20
0
votes
0
replies
104
views
Allele specific expression of imprinted gens from 10x scRNA-seq data
scrna-seq
imprinted
10x
genes
2 days ago by
singcell
• 0
0
votes
1
reply
166
views
When should I use R-MarkDown over R-Script ?
r
rscript
rmarkdown
updated 2 days ago by
ATpoint
82k • written 2 days ago by
Amr
▴ 160
0
votes
2
replies
175
views
LncRNA Nomenclature
ENST
nomenclature
lncrna
GBB
ENSG
2 days ago by
jain72744
▴ 10
0
votes
0
replies
109
views
Nomalization - TCGA, RNA-seq and Microarray
TCGA
RNA-seq
Nomalization
Microarray
2 days ago by
jain72744
▴ 10
6
votes
2
replies
180
views
EdgeR - relationship between logFC and coefficients
differential-expression
r
edger
updated 2 days ago by
Gordon Smyth
★ 7.1k • written 2 days ago by
gBioStar5
▴ 10
2
votes
5
replies
340
views
Importing a fastq file
Fastq
updated 2 days ago by
size_t
▴ 120 • written 3 days ago by
oumo
• 0
3
votes
1
reply
154
views
Question about methylation location
Methylation
WGBS
bisulfide
updated 2 days ago by
dthorbur
★ 1.9k • written 2 days ago by
Eren
• 0
0
votes
0
replies
117
views
Krona Pie-chart taxanomy IDs were not found warning. Taxonomy Classification Metagenomics
Classification
Metagenomics
Krona
Kraken2
2 days ago by
Aytaç
• 0
0
votes
0
replies
130
views
How do I calculate SE or P value if I only have BETA
prscsx
beta
se
pvalue
updated 2 days ago by
zx8754
11k • written 2 days ago by
curious_butterfly
• 0
0
votes
0
replies
124
views
supervised admixture
supervised
admixture
2 days ago by
RT
▴ 10
0
votes
0
replies
125
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Randomization
Mendelian
two-sample
2 days ago by
Nikki
• 0
2
votes
0
replies
127
views
News:
course on Landscape Genomics at the EPFL in Lausanne (June 17-21)
LandscapeGenomics
SNPs
LocalAdaptation
GIS
2 days ago by
carlopecoraro2
★ 2.5k
0
votes
8
replies
381
views
Different output for read length
samtools
BAM
2 days ago by
marco.barr
▴ 100
0
votes
1
reply
346
views
Snakemake fails to find conda in PBS
snakemake
updated 2 days ago by
tim.booth
▴ 60 • written 4 weeks ago by
yixinzeng
• 0
0
votes
2
replies
201
views
Presence of unknown sites in ANNOVAR output file
ANNOVAR
updated 1 day ago by
Ram
43k • written 2 days ago by
sainavyav22
• 0
3
votes
4
replies
282
views
Truncated metadata file report from ENA Portal API
ena
python
1 day ago by
Giulia
• 0
0
votes
0
replies
176
views
What is workflow for de-novo assembling of nuclear and mito genomes of non-model organisms
de-novo
WGS
DNA-seq
assembling
2 days ago by
Matvii Mykhailichenko
• 0
0
votes
3
replies
541
views
JASPAR2024_getMatrixSet error
JASPAR2024
getMatrixSet
updated 2 days ago by
Ram
43k • written 11 weeks ago by
maplewj
▴ 10
185 results • Page
1 of 4
Recent Votes
Answer: joint callset and vcf sorting, unknown TAG issue
Answer: joint callset and vcf sorting, unknown TAG issue
A: what does 'none','unk','incmpl','cmpl' in UCSC refgene tables mean
A: what does 'none','unk','incmpl','cmpl' in UCSC refgene tables mean
Gff To Vcf
Comment: Longest transcript variant per gene
Comment: Longest transcript variant per gene
Recent Locations •
All
UK,
1 minute ago
United States,
2 minutes ago
Austria,
2 minutes ago
Dartmouth College,
3 minutes ago
Russia,
4 minutes ago
United States,
8 minutes ago
UK,
9 minutes ago
Recent Awards •
All
Popular Question
to
Jen
▴ 70
Scholar
to
Pierre Lindenbaum
161k
Popular Question
to
Michael
54k
Popular Question
to
Kai_Qi
▴ 130
Popular Question
to
pramach1
▴ 40
Popular Question
to
vytarasov
▴ 180
Teacher
to
Carlo Yague
8.7k
Recent Replies
Comment: Output file of satools flagstat empty
by
GenoMax
142k
If you posted the entire command line then you did not include `-O $MAPPING/${i}.mapping_stats.txt` in that.
Comment: joint callset and vcf sorting, unknown TAG issue
by
Matteo Ungaro
▴ 100
@Pierre Lindenbaum I see. I looked up and, although present, the TAG goes like this in both files: `##INFO=<ID=1000gALT,Number=1,Type=Strin…
Comment: joint callset and vcf sorting, unknown TAG issue
by
Matteo Ungaro
▴ 100
@Pierre Lindenbaum much appreciated, thanks for the explanation and possible approaches to solve this. I'm not in the position to run `U…
Comment: Tophat multiple or unique mapping criteria
by
Ruqaiya
• 0
> The --b2-mp defines the mismatch penalty: the first number is used when the quality of the base is good, the second when it's bad. If you…
Comment: joint callset and vcf sorting, unknown TAG issue
by
Pierre Lindenbaum
161k
> Still, I can't understand the Invalid tag name: "1000gALT" the following line is missing in the VCF header: ##INFO=<ID=1000gALT,Num…
Answer: joint callset and vcf sorting, unknown TAG issue
by
Pierre Lindenbaum
161k
INFO at 121387974 is .;CpG this is an invalid INFO column. There is an invalid attribute named '.' followed by the attribute CpG, …
Comment: joint callset and vcf sorting, unknown TAG issue
by
Matteo Ungaro
▴ 100
@Pierre Lindenbaum as I don't know the meaning of `.;` and I've seen there are many in both files, I simply removed them with `grep -v`. …
Comment: joint callset and vcf sorting, unknown TAG issue
by
Matteo Ungaro
▴ 100
My bad I switched positions between the two files when looking the first time. They do indeed look abnormal but how can I fix it? Below the…
Comment: Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in py
by
beginner123
• 0
Hi, no I'm using the python implementation as linked above.
Comment: joint callset and vcf sorting, unknown TAG issue
by
Pierre Lindenbaum
161k
Show us the content of the INFO column at the problematic positions.
Comment: Tissue-specific DEG analysis with DEseq2
by
ATpoint
82k
Sounds like full confounding. Be careful. Personally I would not do this comparison. There is no way to distinguish tissue effect from dono…
Answer: input file in rmats
by
Mathew
▴ 90
Hi, In the example they give in their GitHub (https://github.com/Xinglab/rmats-turbo/blob/v4.3.0/README.md): They have 2 sample groups wi…
Comment: Longest transcript variant per gene
by
Mathew
▴ 90
I'm glad it worked well for you! Good luck with the rest of your project. I wish you the best.
Comment: Longest transcript variant per gene
by
sansan_96
▴ 90
Thanks so much
Comment: Longest transcript variant per gene
by
sansan_96
▴ 90
Hello again, It works very well, thank you very much for this solution.
Traffic: 1190 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6