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867 results • Page
1 of 18
Sort: Rank
Rank
Views
Votes
Replies
1
vote
5
replies
405
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
updated 2 hours ago by
arctic
▴ 40 • written 9 days ago by
M.
▴ 30
0
votes
0
replies
29
views
Manual Assembly and Protein Translation, HELP, assignment revision
sequence
university
assembly
protein
genomics
3 hours ago by
rackbersingh
• 0
0
votes
0
replies
63
views
How to remove multiple batch effects from RNA-seq data before limma differential gene expression analysis?
batch
ComBat-seq
limma
RNA-seq
removeBatchEffect
4 hours ago by
t.fortunato.asquini
• 0
0
votes
1
reply
145
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
updated 5 hours ago by
pjb39
▴ 200 • written 2 days ago by
beantkapoor16
• 0
0
votes
2
replies
109
views
Output file of satools flagstat empty
samtools-flagstat
updated 5 hours ago by
Mathew
▴ 100 • written 7 hours ago by
ramendra.sarma
• 0
0
votes
0
replies
41
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
eigencorplot
PCAtools
deseq2
pca
6 hours ago by
BioinfGuru
★ 1.7k
2
votes
8
replies
194
views
joint callset and vcf sorting, unknown TAG issue
sort
bcftools
GLNexus
merge
VCF
updated 6 hours ago by
Pierre Lindenbaum
161k • written 9 hours ago by
Matteo Ungaro
▴ 100
0
votes
0
replies
58
views
News:
Online course: An Introduction to Nanopore Direct RNA Sequencing
Nanopore
RNAseq
13 hours ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
164
views
input file in rmats
rmats
updated 14 hours ago by
Mathew
▴ 100 • written 2 days ago by
Lambodarswain316
• 0
0
votes
1
reply
167
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
updated 22 hours ago by
Mathew
▴ 100 • written 1 day ago by
Christopher
• 0
6
votes
7
replies
240
views
Longest transcript variant per gene
transcript
longest
variant
orthofinder
1 hour ago by
sansan_96
▴ 90
2
votes
2
replies
154
views
error in fun(x((i)), ...) : only defined on a data frame with all numeric alike variables
studio
Cibersort
R
updated 23 hours ago by
Mathew
▴ 100 • written 1 day ago by
Azra
▴ 10
2
votes
1
reply
160
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
216
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
8 hours ago by
beginner123
• 0
6
votes
4
replies
13k
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
89
views
imputation through beagle
panel
beagle
reference
imputation
1 day ago by
analyst
▴ 50
0
votes
1
reply
130
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
6
replies
292
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
plink
bioinformatics
genomics
updated 2 hours ago by
Pierre Lindenbaum
161k • written 1 day ago by
ajbarrett98
• 0
0
votes
11
replies
386
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
1 hour ago by
Tuck898
• 0
1
vote
3
replies
191
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
203
views
what is another word for a BLAST "hit"?
blast
alignment
1 day ago by
dec986
▴ 380
1
vote
2
replies
200
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
149
views
extract viral protein of interest from 10k whole viral genomes
nBLAST
viral-genome
updated 1 day ago by
Ram
43k • written 2 days ago by
Shwetha
• 0
0
votes
0
replies
117
views
Marker Features variance by cluster, sample, and treatment group
Seurat
scATAC-seq
ArchR
updated 1 day ago by
Ram
43k • written 2 days ago by
naomiboldon
• 0
1
vote
3
replies
222
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
532
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 2 days ago by
Pierre Lindenbaum
161k • written 5 days ago by
schmince
• 0
0
votes
5
replies
251
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
2 days ago by
SilhouetteQ
• 0
0
votes
1
reply
141
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
228
views
How are score_weights calculated in this code?
single-cell
1 day ago by
carolofharvest
▴ 40
0
votes
1
reply
179
views
How to convert Haps file to vcf file?
pre-phasing
GWAS
imputation
updated 2 days 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
122
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
155
views
Microbial Signal Transduction Database
MiST
updated 2 days ago by
zx8754
11k • written 2 days ago by
Shravani
• 0
0
votes
1
reply
167
views
DESeq2 error
DESeq2
updated 2 days ago by
ATpoint
82k • written 2 days ago by
sooni
▴ 20
0
votes
0
replies
114
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
177
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
186
views
LncRNA Nomenclature
ENST
nomenclature
lncrna
GBB
ENSG
2 days ago by
jain72744
▴ 10
0
votes
0
replies
120
views
Nomalization - TCGA, RNA-seq and Microarray
TCGA
RNA-seq
Nomalization
Microarray
2 days ago by
jain72744
▴ 10
6
votes
2
replies
191
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
350
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
166
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
128
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
140
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
134
views
supervised admixture
supervised
admixture
2 days ago by
RT
▴ 10
0
votes
0
replies
136
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Randomization
Mendelian
two-sample
3 days ago by
Nikki
• 0
2
votes
0
replies
136
views
News:
course on Landscape Genomics at the EPFL in Lausanne (June 17-21)
LandscapeGenomics
SNPs
LocalAdaptation
GIS
3 days ago by
carlopecoraro2
★ 2.5k
0
votes
8
replies
394
views
Different output for read length
samtools
BAM
2 days ago by
marco.barr
▴ 100
0
votes
1
reply
353
views
Snakemake fails to find conda in PBS
snakemake
updated 3 days ago by
tim.booth
▴ 60 • written 4 weeks ago by
yixinzeng
• 0
0
votes
2
replies
207
views
Presence of unknown sites in ANNOVAR output file
ANNOVAR
updated 1 day ago by
Ram
43k • written 3 days ago by
sainavyav22
• 0
867 results • Page
1 of 18
Recent Votes
A: Get nonoverlapping regions of two bed files
Get nonoverlapping regions of two bed files
Answer: install package
Answer: How I do lift over a Plink bim file from Hg18 to Hg19.
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
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Recent Awards •
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6.4k
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pjb39
▴ 200
Popular Question
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▴ 70
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161k
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54k
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Kai_Qi
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Recent Replies
Comment: Longest transcript variant per gene
by
sansan_96
▴ 90
Thank you very much, success in your projects.
Comment: In IGV is this a heterogeneous mutation or false call?
by
Tuck898
• 0
Thanks for the input :)
Comment: install package: package ‘gmwm’ is not available for this version of R
by
Pine
▴ 20
This seems to indicate that the R verison you are using (or packages it depends on) are not compatible with the R version you are using any…
Answer: Tissue-specific DEG analysis with DEseq2
by
arctic
▴ 40
Not my area of expertise but GTEx portal seems to offer visual comparison of expression across tissues, maybe checking their pipeline could…
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
Pierre Lindenbaum
161k
> I think I am mostly struggling with what would need to be coded to my dataset here and how to run this loop on my set in general. i do…
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
ajbarrett98
• 0
Pierre, I am a novice at all of this in general and I have never used Java-based programming before. I may not be able to properly wrangl…
Answer: Practical Haplotype Graph v2 not finding correct paths
by
pjb39
▴ 200
There have been a couple of bugs found that affect imputation accuracy, one in build-kmer-index and one in find-paths. The find-paths bug o…
Comment: Output file of satools flagstat empty
by
Mathew
▴ 100
Hi, In your samtools flagstat, -o specifies the output format. This can be set to 'default', 'json', or 'tsv'. If -o is not specified , t…
Comment: Tissue-specific DEG analysis with DEseq2
by
BioinfGuru
★ 1.7k
I wrote an R package (see [rrdr.io][1], and [github][2]) some years ago to calculate tissue specificity from bulk RNAseq based on [this pap…
Comment: joint callset and vcf sorting, unknown TAG issue
by
Pierre Lindenbaum
161k
> set the Number= to 0 instead of 1; I'm not sure it's a problem. > probably I should also change the Type to Flag ah yes, my bad ! (f…
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=0,Type=Flag,…
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…
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