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122,217 results • Page
729 of 2445
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
954
views
Need help for selecting the best K value of ADMIXTURE
admixture
population structure
4.8 years ago by
rprog007
• 0
0
votes
0
replies
830
views
Generating Circular RNA FASTA files using CIRI
circRNA
CIRI
circular
RNA
RNA-seq
4.8 years ago by
André Filipe Gonçalves Gabriel
• 0
2
votes
2
replies
1.4k
views
PHG ImputePipelinePlugin with VCF as input is incomplete?
phg
tassel
updated 4.8 years ago by
pjb39
▴ 220 • written 4.8 years ago by
dovi
▴ 60
1
vote
3
replies
3.4k
views
Quast 5.0.2 Problem
assembly
quast
qc
updated 3.5 years ago by
horeyezonr
▴ 20 • written 5.4 years ago by
augustofranco93
• 0
0
votes
2
replies
881
views
PCA analysis using DESEq2 pipeline
rna-seq
R
4.8 years ago by
aranyak111
• 0
4
votes
3
replies
9.2k
views
Samtools bam2fq converting bam file to fastq. What happens to unmapped reads?
Assembly
alignment
sequencing
next-gen
updated 4.8 years ago by
lieven.sterck
16k • written 4.8 years ago by
williamsbrian5064
▴ 540
0
votes
4
replies
1.1k
views
Removing warning FASTQC
next-gen
4.8 years ago by
ipb727258
• 0
0
votes
1
reply
1.4k
views
WGCNA soft thresholding problem
WGCNA
z-score normalization
soft threshold
4.8 years ago by
lilingjoyo
▴ 40
0
votes
0
replies
445
views
Cytoscape Merge Intersection
software error
4.8 years ago by
alekos.biologia
• 0
0
votes
4
replies
4.0k
views
PCA on subset of patients, from 22 separate chromosome vcf files
principal-component-analysis
vcf
PCA
updated 2.7 years ago by
Ram
45k • written 4.8 years ago by
vincentpluimakers
• 0
1
vote
2
replies
944
views
low alignment rate of methyl-seq data
alignment
4.8 years ago by
Sara
▴ 280
3
votes
8
replies
1.7k
views
Puzzling NCBI BLAST+ output after transcriptome assembly
blast
ncbi
fasta
transcriptome
trinity
updated 4.8 years ago by
h.mon
35k • written 4.8 years ago by
ella
• 0
1
vote
1
reply
3.8k
views
Difference between Cosmic Annotation from VEP and directly from COSMIC VCF.
VEP
Annotation
updated 4.8 years ago by
yussab
▴ 100 • written 9.1 years ago by
always_learning
★ 1.2k
0
votes
1
reply
1.2k
views
Counting the number of species from NCBI Taxonomy browser
Taxonomy
NCBI
updated 4.8 years ago by
shenwei356
8.7k • written 4.8 years ago by
adarsh
▴ 70
1
vote
2
replies
1.7k
views
Duplicate SNP IDs in TOPMed Imputation output for gwas data
topmed
gwas
imputation
SNP
snp
updated 4.8 years ago by
Kevin Blighe
★ 90k • written 4.8 years ago by
yy237
▴ 40
2
votes
7
replies
3.0k
views
What to do when transcriptome assembly quality metrics do not concur. How can you decide what assembly is best to annotate and be used as reference?
RNA-Seq
de novo
assembly quality
updated 4.5 years ago by
Dunois
★ 2.9k • written 4.8 years ago by
MBarcelo
▴ 40
1
vote
2
replies
751
views
How much contaminant is too much ?
sequencing
4.8 years ago by
Sus
▴ 40
1
vote
5
replies
5.0k
views
Retrieving all genes associated with a GO term
R
bioconductor
gene-ontology
updated 4.8 years ago by
Jean-Karim Heriche
27k • written 4.8 years ago by
dnyanadas94
• 0
22
votes
20
replies
7.7k
views
Tool:
elPrep 4.0.0, a high-performance drop-in replacement tool for GATK4/Picard/SAMtools for processing SAM/BAM files
sam
bam
bqsr
updated 2.4 years ago by
Ram
45k • written 7.1 years ago by
Charlotte.Herzeel
▴ 150
0
votes
0
replies
621
views
SNP calling in ATAC-seq data
SNP
4.8 years ago by
minotskaya.ea
• 0
0
votes
4
replies
1.3k
views
xml file conversion in R
R
updated 4.8 years ago by
Biostar
20 • written 4.8 years ago by
Kira
• 0
2
votes
1
reply
918
views
zero inflated correlation computation scRNAseq
scRNAseq
correlation
4.8 years ago by
sim.j.baum
▴ 170
1
vote
14
replies
4.5k
views
Cuffmerge error(?) for RNA-seq
RNA-Seq
updated 4.8 years ago by
bioinfonewbie
• 0 • written 7.9 years ago by
bioinfo
▴ 10
0
votes
2
replies
1.7k
views
Normalize bulk-rna seq with median of ratios and DEseq2
rna-seq
normalization
DEseq2
4.8 years ago by
anael.cain
• 0
1
vote
2
replies
1.1k
views
Extract below 100% overlapping intervals among samples from WGS data
WGS
bedtools
GATK
updated 4.8 years ago by
Pierre Lindenbaum
166k • written 4.8 years ago by
FL512
▴ 20
0
votes
0
replies
1.2k
views
How to incorporate outgroup organism for whole genome SNP based phylogeny?
alignment
genome
SNP
phylogeny
phylogenetics
4.8 years ago by
Kumar
▴ 120
0
votes
4
replies
2.2k
views
Highly correlated modules with clinical trait does not cluster together in eigengene dendrogram, WGCNA.
microarray
gene-expression
WGCNA
updated 2.7 years ago by
Ram
45k • written 4.8 years ago by
vipulwagh31
▴ 20
0
votes
0
replies
689
views
get miRNA expression form total RNA data
RNA-Seq
miRNA
4.8 years ago by
aminijavad4
▴ 10
0
votes
3
replies
1.9k
views
plink --interaction --parameters!!
SNP
plink
updated 4.8 years ago by
zx8754
12k • written 4.8 years ago by
hyekyung.hkj
• 0
0
votes
5
replies
1.5k
views
About shell script
script
alignment
updated 4.8 years ago by
zx8754
12k • written 4.8 years ago by
r00628112
▴ 10
0
votes
1
reply
733
views
how to deal with large matrix for heatmap?
R
gene
4.8 years ago by
BioInProg
• 0
1
vote
2
replies
2.3k
views
ATAC-seq bowtie2 alignment and pre-alignment adapter clipping
ATAC-seq
alignment
bowtie2
updated 4.8 years ago by
ATpoint
90k • written 4.8 years ago by
cwwong13
▴ 40
0
votes
0
replies
690
views
ShortStack input files recommendation
sRNA
ShortStack
miRNA
updated 4.8 years ago by
Biostar
20 • written 4.8 years ago by
candron
▴ 10
0
votes
1
reply
1.1k
views
How to deal with the NA results in corr.test using log2(x+1)?
R
cor
log2
4.8 years ago by
diqixiaoyaoer
▴ 20
0
votes
1
reply
1.7k
views
question about MEME suite installation
sudo cpan
MEME
updated 4.8 years ago by
Mensur Dlakic
★ 30k • written 4.8 years ago by
13719756608
• 0
1
vote
2
replies
1.1k
views
Best way to find orthologous gene between two distant species
gene
genome
updated 4.8 years ago by
GenoMax
154k • written 4.8 years ago by
dongzhang0725
• 0
5
votes
7
replies
1.9k
views
Local Blast Error
blast
RNA-Seq
blastn
4.8 years ago by
bry.th
• 0
5
votes
2
replies
1.3k
views
reduce size of string
sequence
shell
python
updated 4.8 years ago by
Biostar
20 • written 7.5 years ago by
Jason
▴ 10
0
votes
0
replies
630
views
number of reads outside exonic regions in an exome sequencing experiment
exome
next-gen
sequencing
4.8 years ago by
prasundutta87
▴ 730
0
votes
2
replies
1.5k
views
HOMER known motif is unpublished
ChIP-Seq
motif
HOMER
motif finding
known motifs
4.8 years ago by
buffealo
▴ 130
0
votes
2
replies
1.1k
views
system commands from R containing single and double quotes
R
bash
4.8 years ago by
noodle
▴ 650
2
votes
7
replies
1.9k
views
Design in DESeq2: measruing effects of treatment while adjusting for sample type
RNA-Seq
R
4.8 years ago by
Ridha
▴ 130
0
votes
1
reply
1.5k
views
gffcompare input file
gffcompare
RNA-Seq
4.8 years ago by
ziziqolo
▴ 10
0
votes
0
replies
736
views
Fasta blast alignment error
alignment
sequencing
updated 4.8 years ago by
GenoMax
154k • written 4.8 years ago by
jahanshahi.amin
• 0
2
votes
1
reply
2.0k
views
GATK HaplotypeCaller Error
RNA-Seq
GATK
HaplotypeCaller
Java
Error
updated 4.8 years ago by
Pierre Lindenbaum
166k • written 4.8 years ago by
julianneradford
▴ 20
1
vote
3
replies
1.9k
views
call variants for every read
alignment
snp
next-gen
updated 4.8 years ago by
Pierre Lindenbaum
166k • written 4.8 years ago by
mimakaev
• 0
0
votes
0
replies
783
views
bcftools isec: tandem mutations
bcftools
isesc
4.8 years ago by
whb
▴ 60
3
votes
5
replies
7.0k
views
pysam error when reading .bam file ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format?
pysam
bam
sam
4.6 years ago by
daewowo
▴ 80
0
votes
0
replies
845
views
missing informations in VCF file (read mapping)
vcf
mapping
samtools
bcftools
updated 4.8 years ago by
Pierre Lindenbaum
166k • written 4.8 years ago by
romain.derelle
• 0
8
votes
9
replies
6.1k
views
how to get database of plants in FASTA format from uniprot
blast
updated 4.8 years ago by
shzhang
▴ 20 • written 8.2 years ago by
majeedaasim
▴ 60
122,217 results • Page
729 of 2445
Recent Votes
Comment: circos plot for genomic features
Answer: How to perform GO enrichment in non-model organisms?
Comment: circos plot for genomic features
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what cause poly-G from NextSeq
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154k
Look inside the `*.log` files to see if you can get additional clues (and post them here, if you can't figure out things). Check for lines …
Comment: Question about QC and scrublet
by
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3.5k
You can run Scrublet before filtering cells with high gene counts and compare the doublet score vs `n_counts_genes`.
Answer: How to perform GO enrichment in non-model organisms?
by
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16k
In first instance you will as you say need to assign GOterms to your genes. eggNOG-mapper is certainly a valid approach to do this indeed. …
Comment: circos plot for genomic features
by
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▴ 140
@colindaven thanks a lot! `clinker` also seems to be a nice/effective tool to do so. It happens we stuble across a work where they used `Ci…
Comment: circos plot for genomic features
by
colindaven
8.1k
Why not use something like Jbrowse2 instead ? https://jbrowse.org/jb2/gallery/ You can load both haplotypes, use minimap2 to create a paf …
Comment: How excactly is the Q30 is calculated?
by
colindaven
8.1k
This is really a question for your instrument provider. Only MGI application specialists and their bioinformaticians can really answer this…
Answer: How excactly is the Q30 is calculated?
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154k
[**Phred quality scores**][1] have been in use since the 1990s and early days of human genome project. They were co-opted in the fastq form…
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by
Matteo Ungaro
▴ 140
@kevin thanks I was experimenting with the following since I already pursued most of the approaches you mentioned and, in practice, they ar…
Answer: Chip-seq analysis Diffbind
by
ATpoint
90k
I think the results are expected. a) n=2 is underpowered, for any assay and in particular for ChIP-seq which has considerable noise. b) you…
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Wu-Sheng Zhang
▴ 10
Hi @arup , after changing the file name following the read length, I can process them using cellranger arc successfully. Thank you very muc…
Comment: Visualize methylation status in Pacbio Hifi read
by
cmdcolin
★ 4.4k
(as the JBrowse dev) I'm glad to hear this. if you see any trouble with it feel free to let me know, I have tried to keep up to date with m…
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Wu-Sheng Zhang
▴ 10
Got it! I will try to switch their name and re-run the cellranger arc. Thank you very much, @arup !
Answer: low quality data or file name swapping -- cellranger arc errors when processing
by
Arup Ghosh
3.5k
The barcode files with 24nt read length W71_LUNGrep2_S6_L001_R3_001.fastq.gz and W71_LUNGrep2_S6_L002_R3_001.fastq.gz should be the R2.
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154k
Each database has their own method of annotation/validation. Depending on resources available there may be a lag between the databases in t…
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by
Wu-Sheng Zhang
▴ 10
Hi @arup , thank you very much for your suggestions, and here are the results -- they seems correct. May I have your suggestions? Thank you…
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