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96 results • Page
2 of 2
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0
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0
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98
views
Differing output: vcftools' --weir-fst-pop and R hierfstats package's varcomp.glob()
vcftools
hierfstats
fst
3 days ago by
S
• 0
0
votes
2
replies
203
views
what should I do if I get a compromised sample of scRNA-seq data?
scRNA-seq
data
snRNA-seq
updated 3 days ago by
ATpoint
78k • written 3 days ago by
wangjb702
• 0
0
votes
0
replies
94
views
Comparing 16S rRNA (culture) sequences with metagenome
metagenome
shotgun
rRNA_culture
16S
updated 3 days ago by
Ram
41k • written 3 days ago by
aswin
• 0
0
votes
4
replies
277
views
Filling gaps in BAM file
bamtools
samtools
gene
bam
updated 2 days ago by
seidel
11k • written 3 days ago by
hemr3
• 0
0
votes
1
reply
148
views
Annotation GTF/GFF Arabidopsis thaliana
Arabidopsis
GFF
GTF
Annotation
3 days ago by
enriquesan
• 0
1
vote
5
replies
312
views
vcftools
vcftools
updated 3 days ago by
Barista
▴ 10 • written 3 days ago by
sevda
• 0
0
votes
0
replies
83
views
How do I pick the best conditions for scATAC-Seq after a series of bulk test runs?
ATAC-seq
3 days ago by
cyril-cros
▴ 940
0
votes
1
reply
144
views
Microbial gene coverage from blast result
gene
coverage
3 days ago by
aanchal.yadav
• 0
0
votes
0
replies
89
views
extracting Uniprot IDs for Kegg pathways
mapping
uniprot
R
kegg
clusterprofiler
3 days ago by
Assa Yeroslaviz
★ 1.8k
0
votes
1
reply
103
views
Funannotate iprscan Creates empty file
funannotate
interproscan
fungus
annotation
4 days ago by
Umer
▴ 50
2
votes
2
replies
222
views
4 Fastq files for a single run generated by 10X
scRNA-Seq
Fastq
SRA
10X
3 days ago by
hkarakurt
▴ 180
0
votes
4
replies
663
views
How to resolve the error of protein lacking a stop codon when using GenomeThreader for homology prediction?
genome
threader
2 days ago by
peanut
• 0
2
votes
5
replies
245
views
kallisto index build difference according to version
index
version
kallisto
updated 4 days ago by
dsull
★ 5.1k • written 4 days ago by
estilo
• 0
0
votes
2
replies
519
views
Understanding gene level copy number data from TCGAbiolinks
CNV
TCGA
updated 4 days ago by
Zhenyu Zhang
★ 1.1k • written 13 months ago by
billyK
• 0
1
vote
3
replies
338
views
Bam files generated with STAR cause a segmentation fault core dump error when used with another tool
RNA-Seq
mapping
updated 4 days ago by
GenoMax
136k • written 4 days ago by
bkffadia
• 0
0
votes
0
replies
118
views
Should I perform eQTL colocalization for just one of eGenes at a time?
colocalization
coloc
eCaviar
eQTL
5 days ago by
maximal_life
▴ 20
4
votes
2
replies
275
views
KEGG DATABASE
DATABASE
KEGG
updated 2 days ago by
jv
★ 1.3k • written 5 days ago by
Sijjil
• 0
0
votes
1
reply
216
views
Issue with genetic QC sex check
plink
6 days ago by
kl
▴ 10
0
votes
0
replies
117
views
BioSQL Unable to remove database using server.remove_database
BioSQL
biopython
Mysql
Python
6 days ago by
Navindu
• 0
0
votes
0
replies
129
views
bootstraped treemix show no migration event
Treemix
Bootstrap
6 days ago by
reza
▴ 300
0
votes
2
replies
1.5k
views
Does GNOMAD use all LOFTEE LoF filters?
loftee
gnomad
LOF
ensembl
vep
updated 6 days ago by
AMARU
• 0 • written 3.8 years ago by
brismiller
▴ 50
0
votes
3
replies
813
views
"MethylKit" package for WGBS data
MethylKit
WGBS
updated 6 days ago by
viveksomya123
• 0 • written 2.4 years ago by
shrinka.genetics
▴ 20
0
votes
0
replies
150
views
is there a way to set colors pallets for glMDSPlot(x)?
Glimma
glMDSPlot
6 days ago by
James
• 0
0
votes
0
replies
135
views
Compute matrix skipping many regions stating not found in compute matrix output
computematrix
Deeptools
6 days ago by
Mehwish
▴ 10
0
votes
0
replies
205
views
How to find promoters (such as GC box and TATA box) in set of genes using bioinformatics analysis ?
promoter
motif
updated 3 days ago by
Ram
41k • written 6 days ago by
shome
▴ 10
0
votes
2
replies
260
views
How to identify CG, CHG, or CHH from MeDIP data
MethylationStudy
CHG
CHH
CG
MeDIP
3 days ago by
Tm
★ 1.1k
0
votes
0
replies
160
views
Significance of several BUSCO target IDs for the same gene
target_id
sequence-ontology
BUSCO
duplication
6 days ago by
CoLa
• 0
0
votes
1
reply
211
views
doubt about usage of megahit
trinity
megahit
updated 6 days ago by
Istvan Albert
99k • written 7 days ago by
meera
• 0
0
votes
5
replies
303
views
calculate nucleotide diversity from whole-genome-sequence data for individual genes
genomics
nucleotide_diversity
vcf
updated 3 days ago by
manaswwm
▴ 490 • written 8 days ago by
J
• 0
3
votes
6
replies
479
views
scRNA-seq: Consistent low number of cells and low fraction reads across the samples
scRNA-seq
cells
mRNA
expression
gene
updated 6 days ago by
jv
★ 1.3k • written 8 days ago by
newbee
▴ 40
1
vote
5
replies
383
views
CHIPSEQ : Cut AND Run , DiffBind Parameters
Cut-Run
DiffBind
ChIP-seq
updated 22 hours ago by
Rory Stark
★ 2.0k • written 9 days ago by
DINESHR
• 0
0
votes
3
replies
309
views
Can FPKM be used to create bar graphs for DEGs?
RNA-seq
updated 3 days ago by
Ram
41k • written 21 days ago by
junli1988
• 0
0
votes
0
replies
196
views
Trouble Adding Log Fold Changes to KEGG Pathway Visualization
KEGG
RStudio
updated 3 days ago by
Ram
41k • written 28 days ago by
ramirj49
• 0
0
votes
0
replies
147
views
Outgroup for 1000 genomes project
haplotype
1000Genomes
phylogeny
updated 21 hours ago by
Ram
41k • written 4 months ago by
Morgan
• 0
0
votes
0
replies
203
views
Haplotype network/phylogeny of 1000 genomes project
haplotype
1000Genomes
phylogeny
updated 21 hours ago by
Ram
41k • written 5 months ago by
Morgan
• 0
0
votes
0
replies
696
views
Generating variant read count matrix, total read count matrix and binary/ternary mutaion matrix for SNV from scDNAseq FASTQ files
SNV
mutationMatrix
tumorPhylogeny
scDNAseq
mutaion
1 day ago by
supernovamik
• 0
0
votes
3
replies
617
views
Gene family classification using RNA-seq data
gene-expression
RNA-seq
gene-family
updated 2 days ago by
Ram
41k • written 8 months ago by
Dion
• 0
0
votes
1
reply
484
views
FASTQ files for 30x 1KGP of Phase 3 data
1000genomes
fastq
updated 20 hours ago by
Ram
41k • written 13 months ago by
Qboy
• 0
1
vote
3
replies
600
views
How to find DEG with deseq2 in R
GSE
RNA-seq
deseq2
updated 2 days ago by
Ram
41k • written 13 months ago by
mresmaeili995
• 0
0
votes
1
reply
512
views
Problems separating and converting molecule files with openbabel
openbabel
updated 2 days ago by
mthm
▴ 50 • written 16 months ago by
smithk
• 0
1
vote
5
replies
1.5k
views
BLAST: overflow error
BLAST
updated 4 days ago by
GenoMax
136k • written 19 months ago by
antoinefelden
▴ 60
0
votes
3
replies
1.0k
views
Error with Ice normalization when running HiC-Pro
Hi-C
HiChIP
HiC-Pro
updated 3 days ago by
Ram
41k • written 2.1 years ago by
Amina
• 0
1
vote
1
reply
366
views
Trinity 'genes' too much
Trinity
RNA-seq
updated 2 days ago by
Ram
41k • written 2.1 years ago by
Hou
• 0
0
votes
2
replies
657
views
Regarding Error query in publically available RNA seq analysis by R studio
GEO
Rstudio
RNA-seq
NGS
updated 2 days ago by
Ram
41k • written 2.2 years ago by
ruddhida
• 0
0
votes
1
reply
690
views
Alternative tool for split'N'trim
SNP
Galaxy
Single-cell
RNA-seq
updated 2 days ago by
Ram
41k • written 3.6 years ago by
aiswaryabioinfo
▴ 30
0
votes
7
replies
4.2k
views
align_and_estimate_abundance.pl (rsem-parse-alignments: /lib64/libz.so.1: version `ZLIB_1.2.3.3' not found (required by rsem-parse-alignments))
RNA-Seq
alignment
software-error
next-gen
sequence
updated 2 days ago by
Ram
41k • written 5.6 years ago by
nasreenbano91
• 0
96 results • Page
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Recent Votes
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out
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Answer: Issue softclipping reads when they belong and don't belong to a common amplicon
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Its bbmap tool callvariants.sh. I think you are right because I did not get such error when I called variants through freebayes.
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again, it's a problem with the variant caller, which is ?
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out
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Not only opposite case but same case nucleotides are also present in vcf fle. ![enter image description here][1] [1]: /media/images/4…
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This is an error in your input vcf file. The REF allele MUST be différent from the ALT allele.
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