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122,217 results • Page
724 of 2445
Sort: Rank
Rank
Views
Votes
Replies
4
votes
8
replies
2.9k
views
Unused argument in R
R
4.8 years ago by
paria
▴ 110
2
votes
8
replies
4.6k
views
Why sortmerna 4.2.0 runs so slow?
RNA-Seq
sortmerna
software error
RNA
rna-seq
updated 4.8 years ago by
Nifaste
▴ 20 • written 5.6 years ago by
tianshenbio
▴ 190
0
votes
1
reply
4.2k
views
rfe function from caret to perform svm-rfe feature selection
R
feature selection
caret
rfe
svm
updated 4.8 years ago by
tzehuey85
• 0 • written 5.1 years ago by
lenC_biotecLover
▴ 90
0
votes
4
replies
1.0k
views
Finding TBP binding sites on Chipseq Data
ChIP-Seq
4.8 years ago by
majeedmj.ict
▴ 20
0
votes
8
replies
1.8k
views
How to split .bed file in R
r
rna-seq
genome
4.8 years ago by
vivianbalagon
• 0
1
vote
3
replies
981
views
Getting matched peptide to CDR3 sequences
RNA-Seq
4.8 years ago by
zizigolu
★ 4.4k
1
vote
6
replies
3.5k
views
DESEq2 error - 'DESeqDataSet' object superclass 'RectangularData' not defined in the environment of the object's class
DESeq2
R
DESeq
updated 4.8 years ago by
Michael Love
★ 2.6k • written 4.9 years ago by
susheelbhanu
• 0
2
votes
2
replies
7.9k
views
Error attaching phenotype in PLINK (fewer tokens than expected)
GWAS
PLINK
4.8 years ago by
absoldini
▴ 10
21
votes
7
replies
28k
views
Kmer Content in FastQC failed
next-gen-sequencing
updated 3.4 years ago by
Ram
45k • written 9.9 years ago by
hurtc.stri
▴ 20
0
votes
0
replies
1.1k
views
WGCNA: how eigengene expression calculated?
wgcna
sequencing
RNA-Seq
4.8 years ago by
Shero
▴ 10
0
votes
0
replies
623
views
CONTRA OUTPUT FILE (GENE.SYM -UNKNOWN)
CNV Calling
Targeted Sequencing
4.8 years ago by
sushumitha6
• 0
0
votes
1
reply
694
views
Can you average values to do WGCNA?
RNA-Seq
WGCNA
R
Gene Network
4.8 years ago by
gerastuff
• 0
0
votes
0
replies
929
views
recover IMG ids from JGI site
JGI
IMG
ids
updated 4.8 years ago by
lieven.sterck
16k • written 4.8 years ago by
sapuizait
▴ 10
1
vote
1
reply
1.0k
views
Bionano Saphyr Structural Variant ID and Genome Assembly
Assembly
genome
updated 2.7 years ago by
Ram
45k • written 4.8 years ago by
dk0319
▴ 70
4
votes
1
reply
1.6k
views
Are there any repository for panel of normal for running Mutect2?
Mutect2
PON
panel of normal
gatk
4.8 years ago by
DareDevil
★ 4.5k
2
votes
2
replies
1.2k
views
Maker Annotation - multiple gene models give same blastp match
genome
annotation
Maker
updated 4.8 years ago by
lieven.sterck
16k • written 4.8 years ago by
MH85
▴ 20
0
votes
0
replies
595
views
Converting VCF file to ms-style output
SNP
genome
sequence
4.8 years ago by
Jamie Watson
▴ 20
0
votes
9
replies
1.7k
views
for loop command
for loop
fasta
updated 4.8 years ago by
lieven.sterck
16k • written 4.8 years ago by
harry
▴ 40
4
votes
6
replies
2.2k
views
GWAS missing p-values
software error
snp
genome
GWAS
logistic regression
updated 4.8 years ago by
hkj7
• 0 • written 6.9 years ago by
emmacomp
▴ 10
0
votes
1
reply
1.0k
views
Database of drugs warnings/risk
DrugBank
database
risk rating
warning
4.8 years ago by
annydisomma20
• 0
0
votes
0
replies
749
views
exomePeak for non-fragmented libraries
exomePeak
4.8 years ago by
blur
▴ 280
1
vote
7
replies
5.3k
views
Using the Homer suite with conda
homer
conda
bioconda
updated 4.8 years ago by
Biostar
20 • written 8.5 years ago by
rioualen
▴ 750
0
votes
1
reply
1.4k
views
overlay of DE data on reactome pathway
pathway
updated 3.6 years ago by
Ram
45k • written 5.8 years ago by
kanwarjag
★ 1.2k
4
votes
3
replies
3.6k
views
Graph viewer for Reactome Pathways
Reactome
Graph-viewer
R
updated 2.9 years ago by
Ram
45k • written 10.5 years ago by
Deepak Tanwar
★ 4.2k
2
votes
2
replies
1.2k
views
R error: could not find function "makeTxDbFromUCSC"
R
RNA-Seq
4.8 years ago by
xiaoleiusc
▴ 140
0
votes
0
replies
987
views
Tool:
MultiLink Analysis: Brain Network Comparison via Sparse Connectivity Analysis
networks
neuroscience
connectome
brain
updated 2.5 years ago by
Ram
45k • written 4.8 years ago by
alex.crimi
• 0
0
votes
0
replies
818
views
Translate evolutionary model for MrBayes
phylogeny
updated 4.8 years ago by
Biostar
20 • written 4.9 years ago by
lagartija
▴ 160
0
votes
0
replies
869
views
How to investigate population structure
GWAS
VCFs
genome
Assembly
4.8 years ago by
Kumar
▴ 170
0
votes
0
replies
1.1k
views
Panel of normals for Mutect2 GRCh37
gatk
broad
mutect2
4.8 years ago by
nhaus
▴ 420
1
vote
1
reply
738
views
Rockhopper tool help
RNA-Seq
R
next-gen
alignment
4.8 years ago by
qstefano
▴ 20
1
vote
3
replies
1.8k
views
RNAseq GO enrichment analysis: GO organism .db
R
RNA-Seq
GO
updated 4.8 years ago by
e.rempel
★ 1.1k • written 4.8 years ago by
Neuls
▴ 20
0
votes
1
reply
946
views
cloud repository of the ICGC
ICGC
collaboratory
AWS
updated 4.8 years ago by
GenoMax
154k • written 4.8 years ago by
Zahra
▴ 110
3
votes
4
replies
3.0k
views
Convert transcript coordinates to genomic coordinates
alignment
4.8 years ago by
vkkodali_ncbi
★ 3.9k
0
votes
1
reply
1.2k
views
ASpli gbCounts() error
RNA-Seq
ASpli
alternative splicing
R
4.8 years ago by
Dominik_H
• 0
1
vote
4
replies
2.4k
views
How to subset a FASTQ file based on a list of sequences
FASTQ filter
updated 4.8 years ago by
Biostar
20 • written 8.7 years ago by
heso
▴ 40
1
vote
5
replies
5.0k
views
Processing KAAS output (lists of KO numbers) into straightforward knowledge
kegg
kaas
updated 3.4 years ago by
Ram
45k • written 9.8 years ago by
antortjim
▴ 10
0
votes
4
replies
2.7k
views
I downloaded SRA toolkit but i cant instal it
gene
sequence
updated 4.8 years ago by
ATpoint
90k • written 4.8 years ago by
s_lamee
• 0
0
votes
1
reply
1.2k
views
bedtools getfasta giving errors
RNA-Seq
genome
next-gen
gene
4.8 years ago by
mithukuntala
• 0
0
votes
5
replies
1.6k
views
Issue when merging FastQ
Fastq
Merging
mapping
SAM
BAM
updated 4.8 years ago by
Biostar
20 • written 4.9 years ago by
gayal25016
• 0
2
votes
1
reply
2.8k
views
Volcano plot of Deseq2 data
rna-seq
4.8 years ago by
aranyak111
• 0
2
votes
7
replies
4.5k
views
How to regress out variants using SCTransform function?
Single-nuclei RNA sequencing
SCTransform
Seurat
4.8 years ago by
paria
▴ 110
0
votes
3
replies
2.2k
views
Extract gene Name, ID, and description from gff3 file
Annotations
updated 4.8 years ago by
Biostar
20 • written 5.0 years ago by
akibio
• 0
2
votes
2
replies
1.2k
views
GEOquerry error, expression dataset is loading as a list
software error
updated 4.8 years ago by
ATpoint
90k • written 4.8 years ago by
angus.j.g.campbell
▴ 10
0
votes
8
replies
3.1k
views
repeat masker output looks weird: 0% for all of repeat squences
genome
sequencing
updated 4.8 years ago by
Michael
56k • written 4.8 years ago by
slin023
▴ 20
1
vote
7
replies
1.8k
views
Problems with the same gene names in R, any help?
R
gene
updated 4.8 years ago by
lessismore
★ 1.4k • written 4.8 years ago by
ymervenuryavuz
• 0
0
votes
2
replies
4.9k
views
[ti_index_core] the chromosome blocks not continuous at line xxxx, is the file sorted? [pos 1]
vcf
index
variant
updated 4.8 years ago by
Biostar
20 • written 7.8 years ago by
shubhra.bhattacharya
▴ 140
4
votes
5
replies
6.3k
views
Is my WGCNA soft threshold (power) too low?
wgcna
RNA-Seq
clustering
network
4.8 years ago by
jfaberha
▴ 50
0
votes
2
replies
1.3k
views
BLAST like output from NGS fastq file
NGS
blast
updated 2.5 years ago by
Ram
45k • written 4.8 years ago by
MSRS
▴ 590
3
votes
3
replies
11k
views
What is the difference between gbk and gbf file?
annotation
prokka
updated 4.0 years ago by
oschwengers
▴ 120 • written 4.8 years ago by
traditionalGuy
▴ 60
0
votes
1
reply
2.1k
views
cellranger aggr troubleshooting
cellranger aggr
multiomics
10x
RNA-Seq
updated 4.8 years ago by
Biostar
20 • written 4.8 years ago by
jbonarot
• 0
122,217 results • Page
724 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 …
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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?
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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. …
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@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
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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
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8.1k
This is really a question for your instrument provider. Only MGI application specialists and their bioinformaticians can really answer this…
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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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@kevin thanks I was experimenting with the following since I already pursued most of the approaches you mentioned and, in practice, they ar…
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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
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cmdcolin
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(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
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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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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
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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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