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122,217 results • Page
723 of 2445
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
858
views
Error when running QoRTs for JunctionSeq
QoRTs
JunctionSeq
RNA-Seq
4.8 years ago by
n.tear
▴ 80
3
votes
1
reply
941
views
Comparing expression of genes within an RNA-seq Experiment to confirm pluripotency
RNA-Seq
updated 3.8 years ago by
Friederike
9.0k • written 4.8 years ago by
noahhelton98
▴ 80
1
vote
3
replies
1.9k
views
How to run nucmer without reference? (viruses metagenomics)
assembly
clustering
metagenomics
virus
nucmer
updated 4.8 years ago by
colindaven
8.1k • written 4.8 years ago by
Arsenal
▴ 160
1
vote
2
replies
2.0k
views
Recommend me R packages for text mining PubMed abstracts
R
text mining
updated 4.8 years ago by
Jean-Karim Heriche
27k • written 4.8 years ago by
JorgeVallejo
▴ 20
3
votes
7
replies
3.4k
views
Trying to refine REST API query
R
ensembl
API
updated 4.8 years ago by
Emily
24k • written 4.8 years ago by
aroso491
• 0
1
vote
4
replies
1.8k
views
Checking ReadGroup name in BAM file error: E26: Hebrew cannot be used: Not enabled at compile time
RNA-Seq
GATK
updated 4.8 years ago by
Pierre Lindenbaum
166k • written 4.8 years ago by
julianneradford
▴ 20
0
votes
0
replies
911
views
FigTree Error: File contains no tree
software error
alignment
4.8 years ago by
philipp.baumann125
• 0
0
votes
0
replies
1.0k
views
MUMmer for structural variant call
MUMmer
structural variants
circlator
4.8 years ago by
rthapa
▴ 90
0
votes
1
reply
991
views
Problem using CNVkit with RNA-Seq Data to call CNV with Ensembl GRCh37 v75 annotation file
RNA-Seq
CNV
CNVkit
4.8 years ago by
lumal29
▴ 80
0
votes
2
replies
6.2k
views
PEPATAC error: ConnectionResetError: [Errno 104] Connection reset by peer
ATAC-seq
PEPATAC
refgenie
updated 4.8 years ago by
nathan
• 0 • written 4.8 years ago by
m.taheri
▴ 50
2
votes
5
replies
1.4k
views
Forum:
Unit test / integration test packages for R for bioinformatic projects?
R
updated 2.7 years ago by
Ram
45k • written 4.8 years ago by
steve
★ 3.5k
0
votes
0
replies
803
views
What is the cut off used in TCGA vcf files for allelic frequency for calling it as somatic?
tcga
vcf
4.8 years ago by
DareDevil
★ 4.5k
0
votes
0
replies
479
views
Filtering of Predicted Transcripts
RNA-Seq
assembly
rna-seq
4.8 years ago by
cc_prolix
• 0
1
vote
2
replies
890
views
filter varaints from vcf sample based on their presence in N number of samples ?
vcf
SNP
alignment
updated 4.8 years ago by
Pierre Lindenbaum
166k • written 4.8 years ago by
hafiz.talhamalik
▴ 350
1
vote
8
replies
2.0k
views
PCA - untreated sample cluster separated
R
bulk-RNAseq
PCA
variability
4.8 years ago by
camillab.
▴ 160
0
votes
2
replies
3.5k
views
Seurat VlnPlot vs PercentageFeatureSet expression level
R
RNA-Seq
4.8 years ago by
Jeffrey3555054
▴ 20
6
votes
7
replies
8.9k
views
grep things and counting line number in R
R
updated 4.8 years ago by
Biostar
20 • written 7.6 years ago by
saadleeshehreen
▴ 140
7
votes
4
replies
2.4k
views
getBM results are not in the same order as the input in the "values" argument
GEO
biomaRt
updated 4.8 years ago by
Kevin Blighe
★ 90k • written 4.8 years ago by
petrandent
▴ 50
0
votes
6
replies
3.2k
views
bedtools genome file
sequencing
bedtools
4.8 years ago by
tom
• 0
0
votes
0
replies
790
views
Using different tools for different database sequences to identify antibiotic resistance genes.
NGS
alignment
metagenomics
antibiotic resistance
4.8 years ago by
dymphan.17phd
▴ 10
6
votes
2
replies
2.4k
views
Find structural variants comparing two assemblies
Assembly
genome
comparative genomics
updated 4.8 years ago by
Shangzhe Zhang
▴ 20 • written 6.2 years ago by
crimsontabaq
▴ 80
6
votes
4
replies
5.3k
views
Are there any tutorials available for Nanostring data differential expression analysis using DEseq2 ?
nanostring
deseq2
limma
updated 2.7 years ago by
Ram
45k • written 4.8 years ago by
DareDevil
★ 4.5k
0
votes
1
reply
1.5k
views
Making PLINK compatible files from VCF file without phenotype information
plink
gwas
vcf
4.8 years ago by
mfshiller
▴ 20
1
vote
2
replies
1.9k
views
Trying to get sequence using sequinr generates error "Error in readLines(socket, n = nelem, ok = FALSE)"
gene
software error
sequence
R
genome
4.8 years ago by
poecile.pal
▴ 50
4
votes
7
replies
2.5k
views
Chunk That Fasta?
FASTA
Python
Chunk
DNA Sequence
updated 4.8 years ago by
Biostar
20 • written 6.1 years ago by
damonlbp
▴ 20
23
votes
6
replies
17k
views
7 follow
Bioinformatics Journal with no publishing fees?
Journal
updated 2.7 years ago by
Ram
45k • written 11.1 years ago by
Abdul Rafay Khan
★ 1.2k
0
votes
4
replies
1.3k
views
multi platform GEO analysis based in expression of one gene
geo analysis
microarray analysis
geo
R
written 4.8 years ago by
amirnavidinia2014
▴ 10
2
votes
6
replies
4.5k
views
PRSice: how to obtain exact list of SNPs used for PRSice.best
PRS
PRSice
PLINK
updated 2.9 years ago by
Sam
★ 4.8k • written 5.1 years ago by
m98
▴ 440
2
votes
7
replies
2.7k
views
Annotate hs37d5 genome calls using VEP
vep
annotation
1kgenomes
hs37d5
written 5.4 years ago by
igor
• 0
0
votes
1
reply
712
views
Find SNPs common to mutants, absent in WT (vcf files)
vcf
bcftools
written 4.8 years ago by
charlesh
• 0
2
votes
6
replies
1.5k
views
GMAP intron control
GMAP
mapping
cDNA
intron
written 4.8 years ago by
ch-h
• 0
1
vote
1
reply
966
views
SRA screening for parasite contamination
blast
data screening
rRNA
parasite
host
updated 4.8 years ago by
Mensur Dlakic
★ 30k • written 4.8 years ago by
e.bessette
▴ 10
0
votes
0
replies
799
views
copy number variation, fisher exact test, gistic2.0
gene
genome
4.8 years ago by
Rob
▴ 180
1
vote
8
replies
1.6k
views
Vcf file extraction
SNP
next-gen
updated 4.8 years ago by
Biostar
20 • written 4.8 years ago by
C4
▴ 30
0
votes
1
reply
777
views
MARVEL all_vogs_hmm_profiles issue
MARVEL
prophage
phage
genomics
updated 4.8 years ago by
Mensur Dlakic
★ 30k • written 4.8 years ago by
ams686
• 0
5
votes
1
reply
728
views
Assigning a new value to a function being called on a variable
R
4.8 years ago by
angus.j.g.campbell
▴ 10
0
votes
0
replies
571
views
Bowtie2 alignment accuracy
alignment
mapping
4.8 years ago by
anabaena
▴ 10
1
vote
1
reply
4.9k
views
Python Script To Do Virtual Screening On Pyrx
pyrx
autodock
updated 2.7 years ago by
Ram
45k • written 13.7 years ago by
Onat
▴ 40
0
votes
11
replies
2.2k
views
Bulk transcriptome RNA-Seq dataset of Human breast cancer
RNA-Seq
rna-seq
dataset
human breast cancer
4.8 years ago by
H. Z. Amini
• 0
0
votes
0
replies
706
views
Population Genetics WGS: how do I know if I have too few individuals?
wgs
sequencing
next-gen
4.8 years ago by
timothy.delory
▴ 20
3
votes
7
replies
15k
views
Seurat Clustering - Cluster Numbers from 1 instead of 0
RNA-Seq
seurat
Cluster
numbering
updated 4.8 years ago by
pjlmac
• 0 • written 5.4 years ago by
David_emir
▴ 500
0
votes
0
replies
1.4k
views
Displaying a controversial phylogenetic tree as a network to explicitate noise-generating branches
phylogenetic-tree
network
genome
updated 2.4 years ago by
Ram
45k • written 7.3 years ago by
Matteo Schiavinato
★ 3.7k
0
votes
0
replies
997
views
Compare fold change and p values for the same gene between different DESeq runs
RNA-Seq
DESeq
R
volcano
single cell
4.8 years ago by
kw486
▴ 50
2
votes
3
replies
1.1k
views
Very strange duplicate output with stand alone blast
BLAST
4.8 years ago by
Firingam
▴ 30
0
votes
5
replies
1.3k
views
How to search for similar sequences in all public metagenomes?
metagenome
updated 4.8 years ago by
Mensur Dlakic
★ 30k • written 4.8 years ago by
Dgg32
▴ 90
0
votes
0
replies
755
views
how to convert ped files to cnv
convertit
cnv
ped
4.8 years ago by
iag.14800108
• 0
0
votes
0
replies
469
views
How to do Annotate the with allele frequency?
genome
alignment
SNP
4.8 years ago by
mvahed
• 0
0
votes
1
reply
1.8k
views
Job:
Fully Funded Doctoral Researcher Position in Data Science & Health
data-science
updated 2.5 years ago by
Ram
45k • written 6.8 years ago by
sichr2
▴ 10
4
votes
3
replies
6.0k
views
Pruning a VCF file and extracting pruned in snps using bcftools
bcftools
SNP
updated 2.5 years ago by
Ram
45k • written 4.8 years ago by
AVA
▴ 40
0
votes
0
replies
987
views
How to subsample SARS-CoV-2 dataset with limited computational resources?
sars-cov-2
subsample
ram
genome
gisaid
4.8 years ago by
fhsantanna
▴ 620
122,217 results • Page
723 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
Answer: How excactly is the Q30 is calculated?
A: PCA in a RNA seq analysis
what cause poly-G from NextSeq
what cause poly-G from NextSeq
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Comment: Issue while running Kenddata.
by
GenoMax
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
Arup Ghosh
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
lieven.sterck
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
Matteo Ungaro
▴ 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?
by
GenoMax
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…
Comment: best practice for diploid variant calling
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.
Comment: ID unifiying across different datasets
by
GenoMax
154k
Each database has their own method of annotation/validation. Depending on resources available there may be a lag between the databases in t…
Comment: low quality data or file name swapping -- cellranger arc errors when processing
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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