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3
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1.2k
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GATK Structural Variants Pipeline - Steps
SV GATK Variant-Calling
updated 16 months ago by 45k • written 16 months ago by ▴ 20
0
votes
0
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572
views
Is it possible to keep gene_id and gene_name columns using Seurat::Read10X?
Seurat single-cell scRNA-seq
updated 16 months ago by 45k • written 16 months ago by ▴ 40
0
votes
1
reply
584
views
GO analysis: Indicate genes corresponding to the pathway
GeneOntoloy GO R
updated 16 months ago by ▴ 180 • written 16 months ago by ▴ 20
0
votes
1
reply
489
views
How to hide label in layout file of MCscan (python version)
MCscan
updated 16 months ago by 154k • written 16 months ago by • 0
0
votes
0
replies
390
views
How to deal with possibly important predictors omitted during the building of an OLS multivariant linear regression model?
multivariant-linear-regression
updated 16 months ago by 45k • written 16 months ago by ▴ 20
0
votes
0
replies
370
views
transcriptome annotation
annotation trinity transcriptome
updated 16 months ago by 45k • written 16 months ago by • 0
0
votes
6
replies
1.1k
views
Why most genes have high padj values
RNA-seq DEG
updated 16 months ago by 45k • written 16 months ago by • 0
7
votes
14
replies
5.0k
views
6 follow
How to find tandem duplications pattern in a DNA sequence
Repeat
updated 16 months ago by ▴ 30 • written 4.4 years ago by • 0
0
votes
1
reply
681
views
PCA Visualization error in R - arguments imply differing number of rows
SNPs PCA GBS LINUX r
updated 16 months ago by 12k • written 16 months ago by • 0
0
votes
4
replies
1.2k
views
GO analysis: p-value range
GO R
updated 16 months ago by 5.1k • written 16 months ago by ▴ 20
3
votes
4
replies
1.2k
views
News: ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
BestTalk PlatformPresentation offtopic
updated 15 months ago by 45k • written 16 months ago by ▴ 20
1
vote
3
replies
1.0k
views
seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from input file
subseq seqtk extractionproblem
updated 16 months ago by 154k • written 16 months ago by • 0
0
votes
0
replies
356
views
Challenges of Affymetrix probe IDs for grouping similar genes to calculate their mean
R Mean Affymetrix Probes Grouping
16 months ago by Maryam • 0
0
votes
4
replies
1.1k
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
rna-seq
16 months ago by Bibi • 0
3
votes
2
replies
1.9k
views
is there a tool to recover corrupted fastq files
fastq short-read
updated 16 months ago by • 0 • written 19 months ago by ▴ 70
0
votes
0
replies
479
views
handling bio replicates for chromHMM
replicates chromHMM
16 months ago by Hasan_Daaboul • 0
0
votes
0
replies
354
views
Tool for within-sample ligand-receptor analysis (bulk RNA-seq) ?
cell-cell communication ligand-receptor self-regulation
16 months ago by DGTool ▴ 290
1
vote
1
reply
697
views
geom_bar issue in ggplot2 with xlim()
geom_bar ggplot2 statistics R
updated 16 months ago by 89k • written 16 months ago by ▴ 20
0
votes
2
replies
1.1k
views
Design for complex RNA-Seq experiment using Deseq2
Model.Matrix RNA-Seq Limma DESeq2 edgeR
16 months ago by Ezequiel • 0
2
votes
0
replies
416
views
Tool: Sequence alignment on split read event such as inversion, duplication and complex nested events.
minimap alignment NGMLR
16 months ago by micah ▴ 30
0
votes
0
replies
434
views
problems in installing rDock
rDock
updated 16 months ago by 45k • written 16 months ago by • 0
1
vote
6
replies
4.3k
views
CellRanger output more cells than specified using --force-cells? Why?
scRNA-seq cellranger
updated 16 months ago by ▴ 30 • written 2.1 years ago by ▴ 940
1
vote
2
replies
1.3k
views
Checking chromosome builds for genotyping data
GWAS Liftover PLINK
updated 16 months ago by ▴ 10 • written 3.9 years ago by • 0
0
votes
0
replies
450
views
Buzzled by retrieving metadata on bioprojects for an organism using "rentrez" package
R
updated 16 months ago by 166k • written 16 months ago by ▴ 30
0
votes
0
replies
394
views
Tera-scale metagenomic coassembly tool
co-assembly Metagenomics
16 months ago by Moinuddin • 0
2
votes
1
reply
743
views
RNAseq coverage vs depth for transcript isoform expression?
RNAseq
updated 16 months ago by ★ 8.3k • written 16 months ago by • 0
0
votes
0
replies
497
views
How can i use ESM-1v ?
VEP ESM-1v
16 months ago by Meto • 0
0
votes
0
replies
423
views
Cell type annotation mixed with other type cells
cell annotation.
updated 16 months ago by 154k • written 16 months ago by ▴ 10
2
votes
3
replies
1.0k
views
Trimming tool
Trimming
updated 16 months ago by 45k • written 16 months ago by • 0
0
votes
0
replies
397
views
sci-RNA-seq
cell single seurat sci-rna-seq counts
16 months ago by kilcdincer ▴ 10
0
votes
0
replies
473
views
genomic region of transcription factor
search HOMER motif
16 months ago by qudrat.nii ▴ 40
1
vote
5
replies
1.1k
views
Reconstruction of locus, order contigs
contigs cluster alignment locus
updated 16 months ago by ★ 3.1k • written 16 months ago by • 0
4
votes
9
replies
2.0k
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA R VARIANCE
updated 16 months ago by ▴ 180 • written 16 months ago by ▴ 20
1
vote
2
replies
2.0k
views
constructing pangenome through psvcp
psvcp pangenome
updated 5 weeks ago by ▴ 20 • written 16 months ago by ▴ 70
1
vote
6
replies
2.0k
views
What marks a De-Novo Genome assembly as FAILED?
nanopore denovo illumina assembly genome
16 months ago by SomeOne ▴ 240
0
votes
4
replies
1.8k
views
How to handle duplicated genes in TCGA data?
TCGA GDC mRNA
updated 16 months ago by ▴ 250 • written 16 months ago by • 0
4
votes
9
replies
1.8k
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch alignment
16 months ago by Gabriel R. ★ 2.9k
0
votes
2
replies
866
views
How to generate table_annovar from VCF input?
vcf annovar
updated 16 months ago by 166k • written 16 months ago by ▴ 70
0
votes
0
replies
399
views
How do I quantify the non-coding transcripts that I have generated after using CPAT,PLEK, and BLAST altogether?
transcript Quantify non-coding
16 months ago by Varsha • 0
0
votes
1
reply
1.0k
views
solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* error: could not open input file /geneInfo.tab #2142
STAR
updated 16 months ago by 154k • written 16 months ago by • 0
0
votes
0
replies
480
views
Help interpreting KEGG module definitions for converting to NetworkX graph
definition kegg module database genomics
16 months ago by O.rka ▴ 750
4
votes
5
replies
5.7k
views
Tool: GRIDSS: the Genomic Rearrangement IDentification Software Suite
Assembly Structural-Variation Variant-Calling
updated 16 months ago by ▴ 520 • written 8.6 years ago by ★ 3.0k
0
votes
4
replies
1.7k
views
Merge clusters in Seurat UMAP
seurat umap
16 months ago by kilcdincer ▴ 10
0
votes
0
replies
427
views
Use of ichor CNA
Dog CNA genome
16 months ago by sainavyav22 • 0
1
vote
0
replies
559
views
News: Course on Manual Genome Curation
Genome-Assembly Pretext-View Manual-Genome-Curation
updated 16 months ago by 45k • written 16 months ago by ★ 2.6k
6
votes
4
replies
1.8k
views
Details on salmon index
Salmon
updated 16 months ago by 7.1k • written 16 months ago by • 0
0
votes
0
replies
460
views
Error when running create-maf-vcf at convertGVCFToHVCFForChrom step - PHGv2
PHG pangenome PHG_v2
16 months ago by Jsarria.EEAD • 0
0
votes
2
replies
703
views
How can I calculate the OS of each patient?
overall-survival
16 months ago by Pedro • 0
1
vote
1
reply
660
views
mitochondrial genome assembly pipeline
mammals mitochondrial-genome
updated 16 months ago by 45k • written 16 months ago by ▴ 30
0
votes
0
replies
490
views
cat-bgen fail
bgenix
updated 16 months ago by 45k • written 16 months ago by • 0
121,932 results • Page 109 of 2439
Recent Votes
What happened to biomart.org
Answer: allele frequency in VCF
Understanding terms, specifically relating to GT:PL in a VCF file
Comment: Looking to learn practical bioinformatics
Answer: WGCNA package in R: dendogram plot error
Answer: Does this adapter content from fastqc to warrant trimming prior to alignment?
Answer: Does this adapter content from fastqc to warrant trimming prior to alignment?
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Recent Replies
Comment: What happened to biomart.org by Jeremy Leipzig 23k
same with geuvadis.org
Comment: real time PCR data analysis by Gordon Smyth ★ 8.3k
Are you doing qPCR for one gene or for several genes?
Comment: protein interaction prediction by Fatemeh ▴ 50
Thanks very much for your help. I need to try it.
Comment: real time PCR data analysis by Fatemeh ▴ 50
Thanks a lot for the link. The problem is that with this repeated measures, if you put the data from different donors in different rows, fo…
Answer: What happened to biomart.org by GenoMax 154k
Looks like EBI let the domain registration expire. The domain was picked up by someone else and turned into the site OP mentions. There use…
Comment: Hifiasm is getting killed while trying to assemble a genome by GenoMax 154k
> I want to reconstruct the assembly using the pacbio reads only. Is there a paper associated with this data? If the original publication/…
Comment: real time PCR data analysis by ATpoint 89k
I think the keyword to go after here is repeated measures https://www.graphpad.com/guides/prism/latest/statistics/repeated_measures.htm
Answer: What happened to biomart.org by ATpoint 89k
Maybe I am missing sth because I've never used the website but only the API and R interface, but I think the website has always been https:…
Comment: protein interaction prediction by Fatemeh ▴ 50
It is most probably binding to a protein. Its function is somehow known though, which is good . Thanks very much for the link. I will have …
Comment: Looking to learn practical bioinformatics by Upesh ▴ 20
ATpoint, you are absolutely bang on. In fact, my intention is not to switch careers but to connect with this field and build tools/systems …
Comment: Hifiasm is getting killed while trying to assemble a genome by pranavdatar01 • 0
I am trying to reproduce the assembly from the raw pacbio reads. I want to reconstruct the assembly using the pacbio reads only.
Comment: Does this adapter content from fastqc to warrant trimming prior to alignment? by ATpoint 89k
I would trim it. Two percent is not much but with WGS, say you have 400mio reads per sample or so, it's still millions of reads that theore…
Comment: Looking to learn practical bioinformatics by ATpoint 89k
> How do I connect the dots to a grand vision of drug discovery, DNA analysis, disease etc. Despite that computational-driven data analys…
Comment: Looking to learn practical bioinformatics by Upesh ▴ 20
Thank you, genomax, for the recommendations! Very helpful!
Comment: Learning Biology/Bioinformatic Basics by Upesh ▴ 20
For anyone landing on this page, the updated link is: [https://www.langmead-lab.org/teaching.html][1] [1]: https://www.langmead-lab.org/…
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