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122,202 results • Page 677 of 2445
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2
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2
replies
2.1k
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making a PCA from MASH distance result
MASH R PCA
4.6 years ago by v.berriosfarias ▴ 140
0
votes
0
replies
727
views
Query on miRDeep2
mirDeep2 mapper
updated 4.6 years ago by 5.8k • written 4.6 years ago by • 0
3
votes
2
replies
2.5k
views
Negative values in Cox regression analysis
survival CoxPH coxregression
4.6 years ago by Amir.Asgary ▴ 30
1
vote
2
replies
1.4k
views
bedtool closest
bedtools
updated 2.4 years ago by 45k • written 4.6 years ago by ▴ 10
3
votes
3
replies
2.1k
views
Visualize DNA sequence as a dot plot?
plot visualization DNA dot
updated 4.6 years ago by 36k • written 4.6 years ago by • 0
0
votes
0
replies
933
views
How should we replace NAs from a genelight object?
R glpca adegenet GBS SNP
4.6 years ago by jaafari.omid ▴ 80
1
vote
1
reply
1.2k
views
Protein-Protein interaction for Upregulated genes
STRING DEGs PPI
updated 4.6 years ago by ★ 30k • written 4.6 years ago by ▴ 20
1
vote
2
replies
1.4k
views
Geno Ontology Analysis
GO hypergtest
updated 4.6 years ago by 35k • written 4.6 years ago by ▴ 20
4
votes
2
replies
2.1k
views
How to retrieve protein sequence from gene ID and output a fasta file
ncbi gene protein biopython entrez
updated 4.6 years ago by 154k • written 4.6 years ago by ▴ 10
0
votes
0
replies
806
views
drug resistance informations for variations
cosmic somatic drug variants germline
4.6 years ago by enes ▴ 40
0
votes
3
replies
1.7k
views
DiffBind consensus peak extraction
DiffBind ChIP-seq
updated 4.6 years ago by ★ 2.2k • written 4.6 years ago by • 0
3
votes
2
replies
2.5k
views
hisat2 output from paired en reads.
hisat2 rna-seq
updated 4.6 years ago by ★ 2.2k • written 4.6 years ago by ▴ 140
5
votes
2
replies
2.9k
views
GATK variant annotation
vcf gatk
updated 4.6 years ago by 45k • written 4.6 years ago by ▴ 40
0
votes
0
replies
849
views
Assembly pipeline/tutorial for SMRT (PacBio) sequenced bacterial genome data?
python perl pipeline genome sequence
4.4 years ago by Kumar ▴ 120
0
votes
0
replies
742
views
MACS2 Summit TSSPlot dividing BDG into bins
TSS Callpeaks MACS2
4.6 years ago by Seigfried ▴ 80
0
votes
0
replies
2.9k
views
Include - in part of the motif for analysis? And "It looks like we don't support this file format" when opening weblogo motif
motif aminoacids sequence biopython weblogo
4.6 years ago by minifoog ▴ 10
0
votes
0
replies
903
views
LD score regression of data including SNPs with extremely low P-value
heritability SNP LDSC
4.6 years ago by Apprentice ▴ 190
0
votes
1
reply
920
views
gRNA concatamer - will it work ?
gRNA CRISPR PAM
updated 4.6 years ago by 90k • written 4.6 years ago by ▴ 10
0
votes
0
replies
1.1k
views
Job: Bioinformatician/Programmer at the University of Pennsylvania
pipelines programmer bioinformatician python r
4.6 years ago by adamnaj • 0
0
votes
0
replies
972
views
Job: Bioinformatician at Turbine / Hungary
proteomics cancerreserach singlecell python r
4.6 years ago by timea.volenter • 0
0
votes
0
replies
1.1k
views
panel of normals for mutect2
mutect2 gatk NGS PoN somatic
4.6 years ago by lait ▴ 180
0
votes
2
replies
3.2k
views
format conversion using OpenBabel
software
4.6 years ago by roybatty269 • 0
1
vote
2
replies
1.2k
views
Program for predicting RNA sequences that may bind to a protein Domain
protein Binding domain RNA
updated 4.6 years ago by ★ 30k • written 4.6 years ago by ▴ 80
4
votes
6
replies
8.2k
views
Understanding TCGA's ASCAT copy number data
tcga ascat copy number
updated 4.4 years ago by ★ 90k • written 4.7 years ago by ▴ 90
0
votes
1
reply
1.1k
views
GDC Data Query
RNA-Seq
updated 4.6 years ago by ★ 1.3k • written 4.7 years ago by • 0
1
vote
6
replies
2.1k
views
Redundancy reduction of de novo transcriptome assemblies with Compacta?
de-novo transcriptome redundancy-reduction
4.6 years ago by Dunois ★ 2.9k
0
votes
5
replies
2.1k
views
Cellranger count.srun issues
cellranger srun
updated 4.6 years ago by 154k • written 4.6 years ago by • 0
2
votes
2
replies
2.8k
views
Up-to-date GWAS Power Calculator and GWAS power comparison
GWAS power
4.6 years ago by moxu ▴ 510
1
vote
1
reply
3.7k
views
How to design WGCNA: one analysis over all sample or seperate analysis (using consensus module analysis)?
WGCNA RNA-seq
updated 4.6 years ago by ★ 90k • written 4.6 years ago by ▴ 20
3
votes
2
replies
1.7k
views
Contradiction in Harzard ratio and Log fold change
LogFC Fold-change Cancer Hazard-Ratio HR
updated 2.2 years ago by 45k • written 4.6 years ago by ▴ 30
0
votes
0
replies
773
views
Refs/tools for protein interactomes
Protein PSI-MI Interactome Orthologs PPI
4.6 years ago by ian.will ▴ 30
0
votes
4
replies
1.6k
views
How to plot a image like this.
Genome R plot Cancer
updated 4.4 years ago by 45k • written 4.6 years ago by ▴ 50
0
votes
1
reply
940
views
How to get Data from https://www.orthodb.org/ by the list of UniprotID
orthoDB
updated 4.4 years ago by 45k • written 4.6 years ago by ▴ 10
1
vote
4
replies
2.0k
views
samtools idxstats unplaced contigs
contig STAR samtools
updated 4.6 years ago by ★ 3.2k • written 4.6 years ago by ▴ 30
0
votes
2
replies
1.2k
views
16S data classification using kraken and centrifuge
centrifuge 16S classification kraken
updated 4.6 years ago by 21k • written 4.6 years ago by ▴ 10
0
votes
3
replies
1.3k
views
Differential expression analysis with LIMMA results
DGE
4.6 years ago by leticia ▴ 20
1
vote
2
replies
1.3k
views
How to parse all the Zn-binding protein sequences from MetalPDB?
PDB database NCBI protein python
4.6 years ago by Kumar ▴ 120
0
votes
0
replies
828
views
How to assemble short DNA sequences using ABYSS?
sequence multiple-alignment assembly
4.6 years ago by anikcropscience ▴ 270
1
vote
5
replies
3.7k
views
How to run SPAdes assembler with bam files?
spades assembler bam
4.6 years ago by marongiu.luigi ▴ 770
2
votes
1
reply
1.7k
views
Filter contig fasta file by GC content
contig gc
updated 4.6 years ago by 154k • written 4.6 years ago by • 0
0
votes
0
replies
866
views
DisGeNET plugin usage error
DisGeNET phenotype plugin vep
4.6 years ago by enes ▴ 40
0
votes
0
replies
771
views
negative BAF values OH
LOH cnvkit BAF
4.6 years ago by John • 0
1
vote
3
replies
2.7k
views
MASURCA output
masurca
updated 4.6 years ago by ★ 3.3k • written 4.6 years ago by ▴ 10
0
votes
0
replies
2.0k
views
Job: Research assistant in straining engineering at DTU Center of Biosustainability
engineering Biofoundry E.coli Strain
updated 2.7 years ago by 45k • written 4.6 years ago by ▴ 90
0
votes
0
replies
2.0k
views
Job: Research assistant for yeast natural products project at DTU Biosustain
yeast preps DNA DTU Biosustain CRISPR
4.6 years ago by info ▴ 90
1
vote
8
replies
2.3k
views
how to select peaks at not transcribed genes
bedtools transcribed peaks not_trasncribed
updated 4.6 years ago by 90k • written 4.6 years ago by ★ 1.3k
0
votes
0
replies
950
views
Job: Analytical chemist (RA) for yeast natural products project at DTU Biosustain
HPLC yeast biochemistry
4.6 years ago by info ▴ 90
21
votes
28
replies
9.5k
views
How to combine 2 incomplete GTF
Cufflinks Cuffcompare GTF Cuffmerge Merge
4.5 years ago by Rafael Soler ★ 1.3k
5
votes
4
replies
1.9k
views
R command worked yesterday, but stalls today?
R
4.6 years ago by cthangav ▴ 110
0
votes
4
replies
2.6k
views
Snakemake with bwa_mem2_mem unable to open the ref file and doesn' t work
bwa-mem2 conda snakemake pipeline
4.6 years ago by aka ▴ 10
122,202 results • Page 677 of 2445
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strong appearing variant not found by haplotypecaller in -ERC mode and deepvariant but with haplotypecaller in normal mode
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Answer: Log2 transformation is well used, but is there a good paper that can be used as
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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 • 0
Got it! I will try to switch their name and re-run the cellranger arc. Thank you very much, @arup !
Comment: 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 • 0
Hi @arup , thank you very much for your suggestions, and here are the results -- they seems correct. May I have your suggestions? Thank you…
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding by samuel.a.odonnell ▴ 640
I don't believe merqury ignores softmasked (lower case) nucleotides so I don't think that is the case. From what it sounds like, during th…
Comment: ID unifiying across different datasets by zizigolu ★ 4.4k
Thanks a lot to be helpful I’m trying to build a complete `UniProtID` to `GeneSymbol` lookup table and I’m running into a wall. I’ve alrea…
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by thomas.heigl.ibk ▴ 20
thanks for the quick reply. i posted the screenshot. gatk-internally, there is still the difference using -ERC or not, priot is getting …
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by thomas.heigl.ibk ▴ 20
here the igv view. showing the histogram for all samples plus the reads for one: ![enter image description here][1] and expanded view of …
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Arup Ghosh 3.5k
Check the read lengths to make sure the files are correct.
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by Pierre Lindenbaum 166k
> Any suggestions or help you could share please, show us an IGV screenshot of the position GATK realign the reads locally, discards read…
Comment: Can i use orthofinder for small protein datasets and not full proteome? by alexandrakortsi • 0
By sequence. Thank you for your response!
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding by xinguok794 ▴ 10
Thank you for your reply! Unfortunately, despite running YAHS with `--no-contig-ec`, the QV value of the resulting FASTA file did not impro…
Comment: Subsetting before QC in Spatial Transcriptomics by Kent ▴ 30
Hi Kevin, Thanks for the detailed explanation. Due to the characteristics of the datasets, we initially used very lenient quality control…
Comment: Midpoint rooting IQTREE newick file moves node support around by Luca Arbore ▴ 10
Thank you very much Kevin, it worked!
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