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122,217 results • Page 722 of 2445
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977
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Method detecting surface / bounday Carbon-alpha (or sidechains) atoms of PDB 3d coordinates / points
pdb amino acid surface coordinates protein
updated 4.8 years ago by ★ 30k • written 4.9 years ago by • 0
1
vote
2
replies
1.3k
views
Blast Azure VM
blast azure vm
updated 4.8 years ago by 154k • written 4.8 years ago by ▴ 80
1
vote
5
replies
3.0k
views
Why full-length sequencing is not possible in UMI-based methods in single-cell RNA-seq
rna-seq sequencing
updated 4.8 years ago by ★ 7.8k • written 4.8 years ago by ▴ 20
57
votes
15
replies
23k
views
14 follow
Bioinformatics And Computer Science
updated 4.8 years ago by ▴ 50 • written 15.3 years ago by ▴ 80
2
votes
5
replies
2.2k
views
Singularity file management
singularity container reproducibility
updated 4.8 years ago by ★ 3.5k • written 4.8 years ago by ▴ 90
0
votes
0
replies
763
views
macs2 error ["AtrributeError"
software error sequence gene RNA-Seq genome
4.8 years ago by a.hayat20 • 0
0
votes
0
replies
1.2k
views
Job: Bioinformatician / Computational Biologist (2 years) - Multi-omics research in oncology - CEA (Grenoble, France)
systems-biology omics oncology
updated 2.7 years ago by 45k • written 4.8 years ago by • 0
2
votes
0
replies
671
views
How to Interpret Author's Methods in this article?
GO
4.8 years ago by Firingam ▴ 30
0
votes
0
replies
1.1k
views
calculate the Pearson correlation coefficient of lncRNA-mRNA pairs in the gene modules based on WCGNA
RNA-Seq sequencing ncrna sequence wgcna
4.8 years ago by Shero ▴ 10
0
votes
3
replies
1.7k
views
Local calculation of residue depth in python and MacOS >10.15.x
python protein structure
updated 4.8 years ago by 154k • written 4.8 years ago by • 0
0
votes
0
replies
1.1k
views
Masurca hybrid assembly throwing Error correction of PE reads failed error
assembly genome
4.8 years ago by Pac314 ▴ 10
0
votes
2
replies
1.0k
views
GeneMania Cytoscape plugin organism
cytoscape genemamia
updated 4.8 years ago by ★ 2.1k • written 4.8 years ago by • 0
0
votes
2
replies
1.5k
views
Find genes in methylation enrichment
dmrcate goregion missmethyl enrichment epic array
updated 4.8 years ago by ★ 2.1k • written 5.4 years ago by ▴ 70
4
votes
1
reply
3.3k
views
VCF AF and %Freq
allele-frequency VCF
updated 2.1 years ago by 45k • written 4.8 years ago by • 0
1
vote
4
replies
4.9k
views
BIOINFORMATICS Problem that i am struggling to solve. Computation of Profile
sequence genome homework
updated 4.8 years ago by 23k • written 4.8 years ago by • 0
0
votes
0
replies
1.1k
views
No annotations in progressiveMauve alignment output
mauve progressiveMauve
4.8 years ago by langziv ▴ 70
0
votes
1
reply
837
views
EUPAN Toolkits error
software error genome
updated 4.8 years ago by ▴ 110 • written 4.8 years ago by • 0
1
vote
6
replies
2.7k
views
Should you include Trimmomatic unpaired reads when assembling by alignment?
alignment assembly sequence
4.8 years ago by RBright21 ▴ 10
2
votes
1
reply
1.3k
views
How to map ENSEMBL Transcript IDs to coding/non-coding/miRNA
RNA-Seq mapping microarray gene expression HTA
updated 4.8 years ago by 20 • written 4.9 years ago by ▴ 100
2
votes
2
replies
6.2k
views
all unique compound structure (SMILES) of PubChem Database
compound pubchem
updated 3.2 years ago by 45k • written 10.3 years ago by ▴ 130
2
votes
2
replies
1.1k
views
Imputation and SNPs pipeline
Imputation SNPs pipeline
4.8 years ago by dzisis1986 ▴ 70
0
votes
1
reply
1.3k
views
GOPLOT FOR CREATING PLOTS IN R
R gene
updated 4.8 years ago by ★ 90k • written 4.8 years ago by ▴ 10
2
votes
2
replies
8.6k
views
Seurat: Assay to use for differential expression in an integrated data
seurat 10x single-cell RNA-Seq
4.8 years ago by firestar ★ 1.7k
4
votes
2
replies
1.8k
views
What would be an error model for PacBio HiFi reads?
Assembly pacbio hifi
4.8 years ago by sebastian.schmidt.helsinki ▴ 10
0
votes
6
replies
1.3k
views
Estimate edit distance to a reference for a subset of bases in reads (bam files)
next-gen bam samtools sequence
updated 4.8 years ago by 166k • written 4.8 years ago by ▴ 30
4
votes
1
reply
1.8k
views
Tool: rBCS & pyBCS: open-source packages to support interactive visualizations of single-cell data
rna-seq single-cell scrna-seq
updated 2.5 years ago by 45k • written 4.8 years ago by ▴ 450
3
votes
2
replies
6.5k
views
error in density plot - methylation EPIC data
R bioconductor
updated 4.1 years ago by • 0 • written 6.7 years ago by ▴ 10
0
votes
0
replies
889
views
How to add coverage plots of 6 samples in Covid viral genome using circos like R packages
R genomic data visualization
4.8 years ago by S AR ▴ 80
1
vote
5
replies
3.8k
views
mummerplot results interpretation
mummer mummerplot alignment bash
4.8 years ago by langziv ▴ 70
1
vote
5
replies
1.6k
views
BCFTools query regex or boolean expression
bcftools
4.8 years ago by User000 ▴ 750
0
votes
2
replies
1.8k
views
How to do pca plot from .eigenvec files from Plink in R
R GWAs Plink
4.8 years ago by anithanagaraj93 ▴ 10
2
votes
2
replies
1.9k
views
Finding single-organism orthologs using NCBI Gene ID
RNA-Seq NCBI orthologs
updated 4.8 years ago by ▴ 60 • written 4.8 years ago by ▴ 90
2
votes
2
replies
1.9k
views
How to ignore "GT" from vcf file
bcftools nanopore medaka
updated 2.5 years ago by 45k • written 4.8 years ago by ▴ 80
6
votes
16
replies
9.5k
views
6 follow
Python script to remove sequences from a fasta file
Python fasta
updated 4.8 years ago by ▴ 80 • written 7.4 years ago by ▴ 70
16
votes
16
replies
6.8k
views
Species identifcation using 16s rRNA
16srRNA fasta
updated 2.2 years ago by 45k • written 4.8 years ago by ▴ 180
0
votes
4
replies
3.1k
views
Deseq2 : Script out of bounds
Genomics deseq2 R
updated 4.8 years ago by 20 • written 4.9 years ago by • 0
4
votes
4
replies
2.2k
views
Limma: how to get the overall logFC from a linear model without contrast?
limma metabolites metabolomics linear model
updated 4.8 years ago by 35k • written 4.8 years ago by ▴ 190
0
votes
1
reply
1.5k
views
Express v_1.5.1 Error: Transcript IDs from MultiFASTA do not match with (SAM/BAM) file.
rna-seq read counts
updated 4.8 years ago by 5.9k • written 4.8 years ago by ▴ 60
0
votes
3
replies
1.4k
views
which tool should be used to call the genotype?
ngs genotype gatk genotype calling variant
updated 4.8 years ago by 20 • written 4.9 years ago by • 0
1
vote
1
reply
1.2k
views
Extract CDS product from Genbank file with coordinate range
sequence genome gene
updated 4.8 years ago by ★ 3.9k • written 4.8 years ago by ▴ 10
0
votes
5
replies
1.5k
views
Optimized genome browser
RNA Genome
updated 4.8 years ago by 16k • written 4.8 years ago by ▴ 110
0
votes
0
replies
555
views
R, package: ldblock, function stack1kg error in opening BCFFile
SNP
4.8 years ago by ting835698 • 0
5
votes
11
replies
3.0k
views
Virsorter running error
next-gen sequencing
updated 4.8 years ago by ▴ 10 • written 5.8 years ago by ▴ 20
2
votes
2
replies
1.4k
views
Adjusting data for covariates
R
updated 2.7 years ago by 45k • written 4.8 years ago by ▴ 20
0
votes
9
replies
1.8k
views
fastqc report and quality check
RNA-seq
updated 2.3 years ago by 45k • written 4.8 years ago by • 0
0
votes
0
replies
976
views
get % of >= Q30 Bases (PF) per index with InterOp
next-gen
4.8 years ago by genya35 ▴ 50
0
votes
7
replies
5.3k
views
MUMmer plot visualization
MUMmer plot
updated 21 months ago by • 0 • written 4.8 years ago by ▴ 90
8
votes
4
replies
4.6k
views
Changing evalue doesn't change the results of blast
blast sequence alignment
updated 4.1 years ago by 45k • written 11.4 years ago by ▴ 290
2
votes
4
replies
925
views
Differences in results of Bowtie2
alignment
updated 4.8 years ago by 154k • written 4.8 years ago by ▴ 10
0
votes
0
replies
1.7k
views
Job: POSTDOC: Comparative genomics of bacterial pathogens (University of Pittsburgh)
postdoc
updated 2.7 years ago by 45k • written 4.8 years ago by ▴ 420
122,217 results • Page 722 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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