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576
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CWL definition modification
CWL Workflow
2.1 years ago by 1769mkc ★ 1.3k
1
vote
4
replies
2.3k
views
clustalw warning: Bisectingkmeans(): Can't split cluster no. xx
clustalo clustalomega clustalw
updated 2.0 years ago by ▴ 130 • written 4.4 years ago by ▴ 40
5
votes
3
replies
1.4k
views
Why do the same genetic variants sometimes result in different amino acids in the REVEL table?
REVEL
updated 2.1 years ago by 4.8k • written 2.1 years ago by ▴ 110
9
votes
12
replies
2.6k
views
T2T fixed GRCg38 gaps and issues, gaps genomic coordinates.
T2T Reference-Genome
2.1 years ago by marinamrbiotech ▴ 10
0
votes
0
replies
1.9k
views
Blog: Exploring PyMol Colors for Molecular Visualization
Colors. PyMol
2.1 years ago by Sunail • 0
0
votes
0
replies
681
views
PLINK command --file mydata --r --matrix only generating .ld file
plink matrix correlation LD
2.1 years ago by KBMP • 0
1
vote
1
reply
1.1k
views
EPIC beadchip array without DMAP files
methylation DMAP array Illumina EPIC
updated 2.1 years ago by ▴ 180 • written 2.1 years ago by • 0
4
votes
2
replies
1.8k
views
Computer equipment for metagenomic analysis
metagenomics storage ubuntu linux memory
updated 2.1 years ago by 89k • written 2.1 years ago by • 0
2
votes
7
replies
1.9k
views
error: BLAST database name is missing. Please edit provean.sh file to add the name.
provean
updated 15 months ago by 45k • written 2.1 years ago by • 0
0
votes
0
replies
616
views
Make a variation record dict from vcf by pysam quickly
pysam python vcf
2.1 years ago by octpus616 ▴ 120
0
votes
0
replies
513
views
Anyone have knowledge of TSS Predator ??
Usage Predator Prediction Plants TSS
2.1 years ago by nikhil ▴ 20
0
votes
1
reply
871
views
BSgenomeForge with "wrong seq names"
R BSgenomeForge Karyoploter
2.1 years ago by _deb • 0
0
votes
0
replies
408
views
Condition matched normal sample to identify variants
WGS
2.1 years ago by Petesview ▴ 10
1
vote
2
replies
1.2k
views
VG node not present in graph
graph variation pangenome vg variation-graph
2.1 years ago by nkls063408 • 0
5
votes
4
replies
2.1k
views
Is there a 1000GP pangenome available?
vg alignment pangenome low-coverage map
updated 2.1 years ago by ▴ 760 • written 2.6 years ago by • 0
0
votes
5
replies
3.4k
views
Job: Bioinformatics Engineer (6 months) in Clinical Bioinformatics, Curie Institute, Paris, France
gene-panel RNA-Seq next-gen
updated 2.1 years ago by ▴ 10 • written 4.7 years ago by • 0
1
vote
3
replies
1.7k
views
CDS phase 0,1,2 in GFF format
gff3 gff cds phasing phase
updated 4 months ago by ▴ 10 • written 2.1 years ago by 166k
0
votes
0
replies
636
views
Pisces doesn't like high-quality reads when there is a soft-clip affecting the full read.
Pisces
updated 2.1 years ago by 89k • written 2.1 years ago by ▴ 110
0
votes
3
replies
2.0k
views
ProbeID to Gene Symbol Mapping in Microarray data analysis using R
R Maping ProbeID-GeneSymbol
updated 2.1 years ago by 89k • written 2.1 years ago by • 0
1
vote
10
replies
2.2k
views
Do monoclonal antibodies have a blocking effect?
block antibody offtopic
updated 2.1 years ago by ▴ 930 • written 2.1 years ago by ▴ 10
1
vote
5
replies
1.5k
views
Creating tx2gene table from sheep transcripts IDs to gene IDs using NCBI annotation file
tx2gene NCBI sheep
updated 2.1 years ago by 45k • written 2.1 years ago by • 0
0
votes
0
replies
637
views
display vcf after giraffe alignment on IGV
vcf. IGV. giraffe
2.1 years ago by Michal • 0
2
votes
2
replies
1.4k
views
so many zero p-values resulted from mageck mle
crispr mle mageck analysis
2.1 years ago by buffealo ▴ 130
1
vote
15
replies
3.1k
views
Single Cell RNA Seq
scTransform Harmony scRNAseq Seurat
2.1 years ago by scRNA2023 • 0
0
votes
2
replies
1.0k
views
error: BLAST database name is missing. Please edit provean.sh file to add the name.
provean
updated 15 months ago by 45k • written 2.1 years ago by • 0
2
votes
3
replies
1.4k
views
Grouping TCGA samples by tumor_tissue_site: Can some groups be merged to decrease the number of groups?
Grouping TCGA
updated 2.1 years ago by ★ 1.3k • written 2.2 years ago by • 0
0
votes
0
replies
1.4k
views
Try to understand better how to set out an effective sample size within the MetagenomSeq package in microbiome
Microbiome
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 30
0
votes
3
replies
1.2k
views
Library generation based on known diversity of specific residues.
library python generation
updated 2.1 years ago by ▴ 50 • written 2.1 years ago by • 0
0
votes
0
replies
495
views
Error processing chr 'chr7': Failed to process variants for MN01972:49:000H5KYMY:1:11102:26356:2968
PISCES
2.1 years ago by ManuelDB ▴ 110
2
votes
2
replies
1.3k
views
how to combine multiple Cellranger count results from a single library
slurm cellranger
2.1 years ago by g744695539 • 0
3
votes
6
replies
2.7k
views
The GATK "The given bam input has no sample names." error
GATK BWA
updated 2.1 years ago by 154k • written 2.1 years ago by ▴ 210
0
votes
4
replies
2.2k
views
how to merge peaks when finished IDR consistency test in ATAC-seq data?
ATAC-seq IDR
updated 2.1 years ago by 45k • written 4.8 years ago by ▴ 40
0
votes
1
reply
902
views
txt files in minfi
differential-methylation-analysis
updated 2.1 years ago by 45k • written 2.1 years ago by • 0
3
votes
5
replies
3.1k
views
News: (18 August - "Enzyme Stability Prediction") A free webinar on on-going CAFA5 (Critical Assessment of Functional Annotation of proteins) challenge
gene-ontology CAFA protein
2.1 years ago by Alexander ▴ 220
1
vote
6
replies
3.6k
views
How to run CallPeaks()
signac
2.1 years ago by Chris ▴ 360
0
votes
3
replies
1.1k
views
Mapping sequence to my genome
sequence
updated 2.1 years ago by 154k • written 2.1 years ago by • 0
17
votes
6
replies
6.0k
views
Are there mm39/GRCm39 blacklist regions?
blacklist
updated 2.1 years ago by 13k • written 3.4 years ago by 6.1k
4
votes
3
replies
1.5k
views
Creating custom GTF file for use with Cellranger with barcode sequences
Cellranger
2.1 years ago by stefano.iantorno ▴ 70
0
votes
0
replies
457
views
calculating the number of parsimony informative sites on a locus basis
alignment fasta
2.1 years ago by diversitree ▴ 10
2
votes
13
replies
3.4k
views
RepeatMasker error when trying to generate repeat sequence distribution pie chart (all code and errors provided)
repeatmasker
updated 2.0 years ago by 45k • written 2.1 years ago by • 0
1
vote
2
replies
2.7k
views
Jupyter notebook installation
Jupyter
updated 18 months ago by ▴ 10 • written 2.1 years ago by ▴ 130
10
votes
13
replies
5.0k
views
Seeking feedback on ChIP-seq normalization method: Calculating scaling factors by dividing input by IP, including spike-in
ChIP-seq spike-in scaling-factor coverage
13 months ago by kalavattam ▴ 380
0
votes
2
replies
870
views
About batch effect in separate library preparation for multiple samples tested on same day
batch-effect
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 40
0
votes
2
replies
2.8k
views
How to choose threshold for scrublet?
rna-seq scrublet
2.1 years ago by bioinfo ▴ 160
0
votes
0
replies
540
views
How to create proper genotype text file format for use in Coancestry from a vcf file
coancestry R
updated 2.1 years ago by 166k • written 2.1 years ago by • 0
0
votes
0
replies
489
views
Merging Methylation data (M-values) with phenotypic data
methylation r lme4
2.1 years ago by hayleyw • 0
10
votes
14
replies
9.2k
views
8 follow
Coverage plot of a complete genome
coverage plot CNV
updated 13 months ago by ▴ 20 • written 4.9 years ago by ▴ 10
1
vote
2
replies
1.3k
views
Minimap2 giving opposite strand orientation than Pychopper
nanopore Pychopper Minimap2
updated 2.1 years ago by ★ 1.3k • written 2.5 years ago by ▴ 10
0
votes
1
reply
822
views
Time-series RNA-seq analysis using DESeq2
RNA-Seq time-course LRT time-series DESeq2
updated 2.1 years ago by 45k • written 2.1 years ago by • 0
1
vote
9
replies
4.4k
views
build databses for genome using snpEff
annotation SNP snpEff
updated 2.1 years ago by • 0 • written 7.2 years ago by • 0
121,965 results • Page 217 of 2440
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Answer: How to create a consensus of a contig with samtools or bbmap?
Comment: Getting just fastqc.zip file?
alternate allele frequency and minor allele frequency
Calculating minor allele frequency for GnomAD VCF file
Hiring FT Remote Nextflow engineer to build ML workflows for cancer genomics
Answer: Gene expression equivalent of polygenic risk score ?
A: TRF output to .gff file
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Comment: How to create a consensus of a contig with samtools or bbmap? by marongiu.luigi ▴ 760
sorry, I have mistaken samtools with spades... running `samtools view -h...` did the trick. Thank you.
Comment: Help with Ideathon by V K • 0
Thank you for the response! Unfortunately this is completely independent and not part of a course. I was asking for some innovative ways to…
Answer: How to create a consensus of a contig with samtools or bbmap? by lieven.sterck 16k
You assembled a genome using samtools ???? that sounds very weird, if not impossible ... The header (SQ lines) is missing from your file b…
Answer: gnomad par region variants by benformatics 4.2k
The XX and XY counts are present on any given variants page.
Comment: Help with Ideathon by Mensur Dlakic ★ 30k
I don't see a single question here. Saying `I need your expert help in figuring out how I can make this analysis useful!` is too open-ended…
Comment: Differences between published differential gene expression results and own analy by ATpoint 89k
Please link the paper, lets see their methods. With human data it can well be that they included something like surrogate variables to damp…
Comment: Differences between published differential gene expression results and own analy by dsull ★ 7.7k
There are many ways to do normalization and one of the correct ways is simply to plug raw counts into deseq2 (the math that deseq2 uses to …
Comment: tximport error (medianLengthOverIsoform) by rfran010 ★ 1.6k
Is it the version number in your data? e.g. ENST00000415118.1 vs ENST00000415118 could be causing the mismatch?
Comment: Differences between published differential gene expression results and own analy by vernonlim98 • 0
So is there any correct way for normalisation? I know limma recommends CPM via limma-voom and DESeq2 just takes in raw counts and does thei…
Comment: Gene expression equivalent of polygenic risk score ? by Picasa ▴ 690
Thanks a lot for your answer. I will check the paper.
Comment: Differences between published differential gene expression results and own analy by dsull ★ 7.7k
If those logFCs are different, then that's a normalization issue. The logFC is straight forward arithmetic (it's simply dividing mean of […
Comment: Differences between published differential gene expression results and own analy by vernonlim98 • 0
Thanks both for your input. It got me to look at the published methodologies more closely, and you guys were right. One paper that I was re…
Comment: Differences between published differential gene expression results and own analy by vernonlim98 • 0
Yes it does not match at all, and those genes that are common in both analysis results have very different logFC and p values
Comment: Errors with RSEM/bowtie2 by Olivia • 0
I am not sure what you mean by this, but I believe that is what I did. With Trinity, I matched all the paired reads together, so they shoul…
Answer: Gene expression equivalent of polygenic risk score ? by GouthamAtla 12k
I don't think something exists out of the box. With variants, we have a 'weight' for each variant on disease risk (obtained through large s…
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