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122,202 results • Page 675 of 2445
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How to increase the size of the top annotation bars in Complexheatmap
plot annotation ComplexHeatmap heatmap
4.6 years ago by mohammedtoufiq91 ▴ 270
0
votes
2
replies
1.9k
views
How to produce overlapping QQ-plot from GWAS results?
R data-visalization GWAS SNP
4.6 years ago by anikcropscience ▴ 270
1
vote
8
replies
5.6k
views
XGBoost on the unbalanced data
unbalanced_data
4.6 years ago by mrashad ▴ 80
5
votes
5
replies
3.7k
views
How to remove all-N sequence entries from fasta file.
awk perl
updated 4.6 years ago by 21k • written 4.6 years ago by ▴ 30
0
votes
1
reply
661
views
Inserting N bases at 5' end of clipped reads
GenomicAlignments Samtools cutadapt Bowtie2
updated 4.6 years ago by 166k • written 4.6 years ago by • 0
2
votes
6
replies
4.2k
views
for loop to filter dataframe based on conditions
r loop filter
4.6 years ago by katinstack • 0
0
votes
0
replies
904
views
Plink2: Determine if allele2 is major or ref
plink2 plink
4.6 years ago by Brynjar ▴ 20
0
votes
0
replies
700
views
How to correctly map CORALL-generated RNA-seq data to a reference genome?
CORALL stranded mapping paired-end RNA-seq
4.6 years ago by niklasjoshua.ebner • 0
3
votes
7
replies
3.0k
views
Can too high of a ChIPQC RiP% be indicative of insufficient stringency in peak calling?
R ChIP-seq ChIPQC
updated 4.6 years ago by 15k • written 4.6 years ago by ▴ 30
2
votes
1
reply
1.6k
views
RPKM and FPKM quality control check and filtration
scRNA-Seq
updated 4.6 years ago by 6.5k • written 4.6 years ago by • 0
1
vote
3
replies
1.9k
views
Lower bound of y-axis hidden in UpSet plot in R, how to avoid this
Plot R UpSet
updated 4.6 years ago by 90k • written 4.6 years ago by • 0
0
votes
3
replies
3.7k
views
No GO-term and no ontology in goseq() output! What am I doing wrong?
goseq GO-term ontology test.cats
updated 3.8 years ago by 45k • written 11.1 years ago by ★ 1.6k
0
votes
2
replies
1.4k
views
Protein Ligand Docking Software Suggestion
Docking software
4.6 years ago by Qinqing • 0
0
votes
3
replies
2.7k
views
beagle error: genotype is missing allele separator
imputation genomics
updated 4.4 years ago by 45k • written 4.6 years ago by • 0
15
votes
15
replies
14k
views
Single cell RNA-seq: how many PCs to use for t-SNE/UMAP?
umap pca scRNA-seq t-sne RNA-seq
4.6 years ago by MutationalMeltdown ▴ 200
1
vote
2
replies
1.8k
views
Mapping EntrezId to Ensembl IDs returns NA for pseudogenes and snoRNA
RNAseq AnnotationDbi
updated 4.6 years ago by ▴ 390 • written 4.6 years ago by • 0
1
vote
5
replies
2.2k
views
Blastn in galaxy
Blastn galaxy
updated 20 months ago by 45k • written 4.6 years ago by • 0
6
votes
12
replies
5.5k
views
7 follow
Multiqc raises the "cannot import name 'gcd' from 'fractions'" error
multiqc linux rna-sq
updated 4.6 years ago by ★ 1.5k • written 4.6 years ago by • 0
0
votes
5
replies
1.7k
views
How to filter reads only with single SNV
filtering_reads SNV amplicon_sequencing SNP
updated 4.6 years ago by 154k • written 4.6 years ago by • 0
0
votes
4
replies
1.6k
views
Bioinformatics researcher looking for an answer on edgeR and DESeq2
rna-seq R edgeR gene
updated 4.6 years ago by 7.6k • written 4.7 years ago by • 0
3
votes
0
replies
1.0k
views
Using bulk RNA-seq deconvolution as covariates in bulk RNA-seq differential expression analysis
cibersort dwls deconvolution
4.6 years ago by telroyjatter ▴ 240
0
votes
0
replies
1.0k
views
How to produce multiple sequence alignment figures with phenotypic data?
alignment multiple-alignment sequence
4.6 years ago by anikcropscience ▴ 270
4
votes
5
replies
2.2k
views
6 follow
Looking for a Whole Genome Sequencing GrCH38 Control group of roughly 250 samples
wgs control whole
updated 4.6 years ago by 2.9k • written 4.6 years ago by ▴ 20
0
votes
1
reply
2.6k
views
how to run and use the ENCODE ATAC-seq pipline
ATAC-seq ENCODE peak
updated 4.6 years ago by 23k • written 4.7 years ago by ▴ 40
4
votes
4
replies
2.0k
views
htseq-count Error '_StepVector_Iterator_obj' object has no attribute 'next'
htseq-count
updated 4.0 years ago by • 0 • written 4.6 years ago by ▴ 20
1
vote
1
reply
1.3k
views
Rare cell population in single cell ATAC-Seq
atac-seq atac
updated 4.6 years ago by ▴ 110 • written 4.6 years ago by ▴ 800
0
votes
1
reply
1.6k
views
How to get GSE data into IGV
ChIP-Seq IGV GSE
updated 4.6 years ago by ▴ 110 • written 4.6 years ago by • 0
0
votes
8
replies
2.5k
views
Split fasta based on symbol and numeric position in header
python fasta sequence genome split
4.6 years ago by Nick Scales • 0
0
votes
0
replies
817
views
Detecting mono-allelic expression in RNA-seq in human
binomial allele_specific gene_expression rna-seq
4.6 years ago by heskett ▴ 110
4
votes
4
replies
2.2k
views
Is Biopython a Package or Library?
Biopython Python
updated 3.0 years ago by 45k • written 4.6 years ago by ▴ 140
2
votes
2
replies
1.2k
views
Genes with identical reads mapping values across all samples - Kallisto
gene Kallisto expression
updated 4.6 years ago by 56k • written 4.6 years ago by 3.9k
0
votes
0
replies
924
views
Compare segment data produced by CopywriteR and similar tools
copywriter cna
4.6 years ago by Ram 45k
1
vote
1
reply
749
views
R libraries to match SNPs by positions (including switching and flipping)
R Bioconductor SNP
updated 4.6 years ago by 45k • written 4.6 years ago by ▴ 20
3
votes
2
replies
1.2k
views
Is anticancer action of HDAC inhibitors - cancer cells specific or it may cause death to other cell types ?
cancer
updated 4.6 years ago by 27k • written 4.6 years ago by ▴ 220
0
votes
0
replies
707
views
How to incorporate the GRM into a mixed linear model
gwas GRM animal_model
4.6 years ago by DIMITRIOS • 0
0
votes
0
replies
2.1k
views
Job: Group Leader Computational Cancer Biology - VIB-KU Leuven, Belgium
vib groupleader cancer biology computational
4.6 years ago by leen.notebaert • 0
0
votes
4
replies
1.8k
views
sequence similarity
blast linux fasta
updated 4.6 years ago by 22k • written 4.6 years ago by • 0
0
votes
3
replies
3.7k
views
Tassel5v2 vcf file with 'N' in reference and alternate allele
Tassel5v2 SNPcalling GBS
updated 4.6 years ago by • 0 • written 6.1 years ago by ★ 1.1k
0
votes
0
replies
762
views
Calculate accuracy for a Cox model in R
accuracy cox prediction survival R
4.6 years ago by nolwenn ▴ 10
0
votes
0
replies
759
views
News: Online Training - Microbial Metabarcoding - 4-8 October
MicrobialEcology metabarcoding
updated 4.4 years ago by 45k • written 4.6 years ago by ★ 2.7k
1
vote
2
replies
1.5k
views
DEG list turn into keggscape
Cytoscape RNA-Sequencing
4.6 years ago by ashwing.kofficial ▴ 10
0
votes
5
replies
2.8k
views
How to calculate bam coverage apart from Qualimap?
bam qualimap coverage
4.6 years ago by marongiu.luigi ▴ 770
0
votes
0
replies
896
views
Interpreting partial dependence plots
machinelearning caret partialdependenceplot pdp R
4.6 years ago by fana ▴ 40
1
vote
1
reply
1.7k
views
Do I need to assume differences in coverage profile when I compare the first reads from paired end data with single end read data?
single-end paired-end sequencing mapping coverage
updated 4.6 years ago by 154k • written 4.6 years ago by • 0
5
votes
8
replies
2.9k
views
Loading PCA - different value depending on the package used
factormineR PCAtools pca prcomp loadings
updated 4.6 years ago by ★ 90k • written 4.6 years ago by ▴ 160
0
votes
3
replies
1.6k
views
Gigabase Clarification (Same as Gigobyte?)
genomics
4.6 years ago by joe_genome ▴ 70
1
vote
4
replies
2.3k
views
Create Mutational signature plot from vcf file.
R python mutational
4.6 years ago by nhaus ▴ 420
2
votes
1
reply
2.1k
views
Why bamToFastq returns empty fastq files?
bamToFastq error bam fastq
updated 4.6 years ago by 90k • written 4.6 years ago by ▴ 770
0
votes
2
replies
991
views
16S Barcoding long and short sequences return different BLAST results
barcoding 16S
4.6 years ago by robert.murphy ▴ 110
0
votes
0
replies
1.0k
views
how to sort out regions with corresponding scores using computematrix?
computematrix deeptools plotheatmap
4.6 years ago by jiekwo1 • 0
122,202 results • Page 675 of 2445
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strong appearing variant not found by haplotypecaller in -ERC mode and deepvariant but with haplotypecaller in normal mode
Answer: How can I easily remove overlapping transcripts, keeping only longest transcript
Answer: Log2 transformation is well used, but is there a good paper that can be used as
Answer: Flatten a GTF
Answer: RNA-seq - Creating SAF from NCBI gff for Subread featureCounts - keep 'gene' or
Can EdgeR of DeSeq be used for Single-cell RNA-seq?
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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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