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122,217 results • Page 723 of 2445
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0
replies
858
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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 9.0k • written 4.8 years ago by ▴ 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 8.1k • written 4.8 years ago by ▴ 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 27k • written 4.8 years ago by ▴ 20
3
votes
7
replies
3.4k
views
Trying to refine REST API query
R ensembl API
updated 4.8 years ago by 24k • written 4.8 years ago by • 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 166k • written 4.8 years ago by ▴ 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 • 0 • written 4.8 years ago by ▴ 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 45k • written 4.8 years ago by ★ 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 166k • written 4.8 years ago by ▴ 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 20 • written 7.6 years ago by ▴ 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 ★ 90k • written 4.8 years ago by ▴ 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 ▴ 20 • written 6.2 years ago by ▴ 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 45k • written 4.8 years ago by ★ 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 20 • written 6.1 years ago by ▴ 20
23
votes
6
replies
17k
views
7 follow
Bioinformatics Journal with no publishing fees?
Journal
updated 2.7 years ago by 45k • written 11.1 years ago by ★ 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 ▴ 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 ★ 4.8k • written 5.1 years ago by ▴ 440
2
votes
7
replies
2.7k
views
Annotate hs37d5 genome calls using VEP
vep annotation 1kgenomes hs37d5
written 5.4 years ago by • 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 • 0
2
votes
6
replies
1.5k
views
GMAP intron control
GMAP mapping cDNA intron
written 4.8 years ago by • 0
1
vote
1
reply
966
views
SRA screening for parasite contamination
blast data screening rRNA parasite host
updated 4.8 years ago by ★ 30k • written 4.8 years ago by ▴ 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 20 • written 4.8 years ago by ▴ 30
0
votes
1
reply
777
views
MARVEL all_vogs_hmm_profiles issue
MARVEL prophage phage genomics
updated 4.8 years ago by ★ 30k • written 4.8 years ago by • 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 45k • written 13.7 years ago by ▴ 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 • 0 • written 5.4 years ago by ▴ 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 45k • written 7.3 years ago by ★ 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 ★ 30k • written 4.8 years ago by ▴ 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 45k • written 6.8 years ago by ▴ 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 45k • written 4.8 years ago by ▴ 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
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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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Recent Replies
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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