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1,000 results • Page
2 of 20
Sort: replies
Rank
Views
Votes
Replies
4
votes
12
replies
3.5k
views
How to read VCF (v4.1) file? (student project) (samtools version 0.1.19)
variant-calling
samtools
VCF
BCF
updated 27 days ago by
Ram
43k • written 5.5 years ago by
c.clarido
▴ 110
4
votes
12
replies
7.7k
views
6 follow
BWA error: no ID within the read group line
bwa
readgroups
RG
parallel
updated 10 weeks ago by
mgdrnl
▴ 10 • written 3.4 years ago by
whb
▴ 60
3
votes
12
replies
482
views
struggle to get fasta files from ucsc goldenPath
ucsc
getfasta
fasta
20 days ago by
Lila M
★ 1.2k
0
votes
12
replies
3.3k
views
comparative analysis of two strains of bacteria's genomes
genome
gene
updated 11 months ago by
Ram
43k • written 6.5 years ago by
fonteneaudam
▴ 20
2
votes
12
replies
3.3k
views
WCGNA installation help
R
WGCNA
updated 11 weeks ago by
Ram
43k • written 4.9 years ago by
prekrish
• 0
6
votes
12
replies
2.0k
views
Help with error in cellranger
Cellranger
updated 11 months ago by
GenoMax
141k • written 11 months ago by
Chris
▴ 260
7
votes
12
replies
1.6k
views
How to pass arguments in a bash script to perform read alignment to the reference?
exome
bwa
bash
updated 5 months ago by
Ram
43k • written 4.2 years ago by
Karma
▴ 310
0
votes
11
replies
1.1k
views
Normalization for microarrays >1000+ samples?
microarray
normalization
oligo
7 months ago by
evmae
• 0
2
votes
11
replies
1.0k
views
Data preparation for a ML model
machine-learning
RNA-Seq
R
python
biomarkers
4 months ago by
sil_bioinfo
▴ 40
1
vote
11
replies
1.2k
views
Quantification after transcriptome assembly with Trinity
De-novo-transcriptome-assembly
Trinity
RNA-seq-analysis
updated 7 months ago by
GenoMax
141k • written 7 months ago by
langziv
▴ 50
4
votes
11
replies
1.6k
views
Check Strandedness
Check_Strandedness
how_are_we_stranded_here
leafcutter
bash
updated 6 months ago by
Brian Bushnell
20k • written 8 months ago by
Y
• 0
0
votes
11
replies
774
views
Filtering VCF based on codon-transcript
vcf
bcftools
updated 5 weeks ago by
barslmn
★ 2.1k • written 6 weeks ago by
avelarbio46
▴ 30
4
votes
11
replies
619
views
Remove X in row name with only number
GSVA
updated 11 weeks ago by
Ram
43k • written 11 weeks ago by
Chris
▴ 260
2
votes
11
replies
751
views
Reference Guided genome assembly
tabix
updated 8 weeks ago by
Michael
54k • written 8 weeks ago by
sainavyav22
• 0
5
votes
11
replies
1.3k
views
Interpret IGV output inversion
variant-calling
IGV
alignment
updated 8 months ago by
cmdcolin
★ 3.8k • written 8 months ago by
pablo
▴ 300
0
votes
11
replies
1.6k
views
count file having zero
RNA-Seq
next-gen
alignment
updated 10 months ago by
Ram
43k • written 5.2 years ago by
BioBaby
▴ 20
4
votes
11
replies
1.8k
views
PCA WITH PLINK
PLINK
updated 8 months ago by
Kevin Blighe
87k • written 8 months ago by
Michelle Guerra
• 0
0
votes
11
replies
2.2k
views
i want to convert .ht2 files into FASTA file
GATK
HISAT2
FASTA
updated 10 months ago by
Ram
43k • written 4.9 years ago by
saumya.sharma1509
• 0
5
votes
11
replies
989
views
Make heatmap for RNA-seq with non replicate
RNA-seq
updated 8 months ago by
Ram
43k • written 8 months ago by
Chris
▴ 260
2
votes
11
replies
5.2k
views
How long it takes to run repeat masker on a full genome
Assembly
updated 3 months ago by
e.r.zakiev
▴ 200 • written 7.8 years ago by
CAnna
▴ 20
1
vote
10
replies
1.1k
views
Do monoclonal antibodies have a blocking effect?
block
antibody
offtopic
updated 8 months ago by
Jeremy
▴ 880 • written 8 months ago by
jinyu
▴ 10
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 6 days ago by
Ram
43k • written 7.4 years ago by
linda
• 0
1
vote
10
replies
3.1k
views
How to specify/calculate subject coverage of the alignment (alignment of query[protein sequence] and subject[Nucleotide sequence]) in tBLASTn?
alignment
BLAST
tBLASTn
updated 11 months ago by
Ram
43k • written 5.1 years ago by
Kumar
▴ 120
0
votes
10
replies
935
views
ONT Raw Read Sequencing Pipeline
remora
dorado
ONT
Basecall
3 months ago by
turcoa1
• 0
5
votes
10
replies
1.3k
views
the distribution of log2Fc and t value are not similar for bulk RNA-seq
decoupleR
RNA-seq
8 months ago by
alwayshope
▴ 40
2
votes
10
replies
807
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated 25 days ago by
Ram
43k • written 8 weeks ago by
Sky
▴ 10
0
votes
10
replies
601
views
Nextflow ERROR : Timeout waiting for connection from pool
nextflow
21 days ago by
dzisis1986
▴ 70
0
votes
10
replies
852
views
Problem running scPred
scPred
scPredict
updated 5 weeks ago by
Ram
43k • written 3 months ago by
Nitin
• 0
14
votes
10
replies
895
views
How to remove center population from seurat cluster
single-cell
4 months ago by
synat.keam
▴ 100
8
votes
10
replies
2.0k
views
PyWGCNA
WGCNA
10 months ago by
yoshifumimiya
▴ 40
1
vote
10
replies
1.2k
views
Coverage histogram query
Alignment
8 months ago by
prasundutta87
▴ 660
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma
microarray
DEA
batch-effect
updated 5 days ago by
Ram
43k • written 4.7 years ago by
asalimih
▴ 60
3
votes
10
replies
1.2k
views
STAR index not working
STAR
RNA-Seq
7 months ago by
camillab.
▴ 160
1
vote
10
replies
1.7k
views
Deepvariant variant calling by singularity
deepvariant
singularity
conda
docker
updated 7 months ago by
jeffhsu3
• 0 • written 9 months ago by
fra.r.silvestro
▴ 10
5
votes
10
replies
842
views
Error when viewing a bam file
samtools
updated 10 months ago by
Ram
43k • written 11 months ago by
Chris
▴ 260
2
votes
10
replies
3.2k
views
6 follow
Split plink files by a number of SNPs
GWAS
SNP
plink
updated 6 months ago by
Raygozak
★ 1.4k • written 5.8 years ago by
kakukeshi
▴ 80
8
votes
10
replies
682
views
bash script
whole-genome-sequencing
updated 7 days ago by
Ram
43k • written 14 days ago by
bestone
▴ 30
1
vote
10
replies
968
views
file conversion from gtf to gff3 for evidence modeler
gff3
stringtie
gtf
6 months ago by
rj.rezwan
• 0
0
votes
9
replies
753
views
how to use multiple command in one line with using the output of last command to the next
bedtools
linux
bed
4 months ago by
sata72
• 0
0
votes
9
replies
474
views
Low number of both surviving reads after trimming
trimmomatic
trimming
25 days ago by
Jay
• 0
1
vote
9
replies
2.1k
views
kallisto bootstrap / condo installation problem
hfd5
kallisto
condo
updated 12 months ago by
dsull
★ 5.8k • written 12 months ago by
micecanfly
▴ 10
7
votes
9
replies
1.1k
views
Calculation of TMB on gene level
genomics
updated 6 months ago by
svp
▴ 680 • written 7 months ago by
smrutimayipanda
▴ 20
1
vote
9
replies
608
views
Approach for multi species comparative transcriptomics and differential expression analyses
DE
RNA-seq
transcriptomics
updated 3 months ago by
dthorbur
★ 1.9k • written 3 months ago by
fish_enthusiast
• 0
3
votes
9
replies
667
views
STARsolo seg fault without readMapNumber flag
STAR
RNA-seq
STARsolo
Velocyto
updated 6 months ago by
Ram
43k • written 6 months ago by
rbronste
▴ 420
0
votes
9
replies
1.7k
views
WCGNA to Cytoscape
wgcna
cytoscape
rna-seq
updated 11 weeks ago by
Ram
43k • written 3.7 years ago by
ovariohisterectomia
▴ 40
2
votes
9
replies
7.5k
views
6 follow
Read MAP and PED files in PLINK
GWAS
PLINK
updated 4 months ago by
GenoMax
141k • written 6.0 years ago by
ft821525
• 0
2
votes
9
replies
1.2k
views
Salmon (or other pseudo-mappers) for multi-species RNAseq read filtering
STAR
Salmon
mapper
aligner
RNAseq
4 months ago by
ian.will
▴ 30
3
votes
9
replies
780
views
Understanding this analysis pipeline
reads
updated 9 months ago by
Ram
43k • written 9 months ago by
artemchuki
• 0
0
votes
9
replies
975
views
gene id
gene-id
NCBI
updated 9 months ago by
GenoMax
141k • written 10 months ago by
safeassli
• 0
0
votes
9
replies
1.2k
views
Normalization across different single cell RNAseq experimetns
global-scaling
single-cell
scRNA-seq
batch-effect
updated 6 days ago by
Ram
43k • written 3.9 years ago by
jmah
▴ 20
1,000 results • Page
2 of 20
Recent Votes
Comment: Correlation for ATAC-Seq and Chip-Seq
Answer: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Answer: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Answer: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Answer: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Comment: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Answer: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
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Recent Replies
Comment: Redirection of Duplicate PMIDs
by
LauferVA
4.2k
let me know the scope and scale of the request (e.g. I need to do this for every record in Pubmed) and can help
Comment: Redirection of Duplicate PMIDs
by
LauferVA
4.2k
how is this query itself originating?
Comment: Redirection of Duplicate PMIDs
by
dominickd
• 0
I was able to come up with a workaround using the requests library: import requests pmid = 30134295 url = 'https://pubmed.ncbi…
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
by
HyperEvo
• 0
Thanks for you answer! Actually I have already filtered my peak according to blacklist by bedtools. You mean it's meaningless to compare on…
Answer: Redirection of Duplicate PMIDs
by
GenoMax
141k
More than likely not since the database query seems to work for the redirected PMID but not the original. $ esearch -db pubmed -query …
Comment: DYH17 Structure Prediction
by
anasjamshed
▴ 120
Blast showed PDB: 8J07_n9(human) as best template with 62.99%. I also used swissmodel to model the protein and it showed: https://swissmod…
Comment: How to slice a gvcf file with tabix?
by
Pierre Lindenbaum
161k
No, in haplotypecaller
Comment: How to slice a gvcf file with tabix?
by
Sd
• 0
Then what is the best way to do slicing for 1Mb windows? Doing `--intervals` in the GenomicsDBImport?
Comment: How to slice a gvcf file with tabix?
by
Pierre Lindenbaum
161k
> What is your suggestion to run GenomicsDBImport efficiently? call the GVCF by slices eg: chr1:1000000-2000000<br> run GenomicsDBImport …
Comment: How to slice a gvcf file with tabix?
by
Sd
• 0
I want to run gatk `GenomicsDBImport` tool to build a GenomicsDB. I want to slice it to reduce the computation time since I have 1300 gvcf …
Comment: Problem to remove subset of patients with plink
by
chrchang523
10k
The first step has to be taken outside of PLINK here. E.g. append "_1" and "_2" to the duplicated IDs in the .ped or .fam file, then menti…
Comment: Error in cnetplot enrichplot package
by
Ram
43k
Show us the exact call to `cnetplot()` with a sample of all input parameters. Did you compare notes with your friend?
Answer: How to slice a gvcf file with tabix?
by
Pierre Lindenbaum
161k
why would you need to slice a gvcf file ? all the tools in gatk can use a BED / interval / chromosome to narrow the analysis
Comment: Error in cnetplot enrichplot package
by
Farhad
• 0
I check dataframe it has more than 2 columns
Comment: Error in cnetplot enrichplot package
by
Farhad
• 0
We write it to csv and then send it via email
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