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121,898 results • Page 626 of 2438
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3
votes
3
replies
2.3k
views
Bcftools isec output only contains one sample name - how to identify which samples share the same variants
bcftools vcf isec
updated 4.2 years ago by 89k • written 4.2 years ago by ▴ 80
1
vote
1
reply
954
views
What tools are best for conjoined gene/readthough detection and how do they differ from fusion gene detection?
conjoined fusion gene
updated 4.2 years ago by 48k • written 4.2 years ago by 23k
2
votes
3
replies
1.3k
views
Retrieving the corresponding Haplotype CDS from Ensembl
gene Ensembl protein Haplotype
updated 4.2 years ago by 24k • written 4.2 years ago by ★ 3.0k
0
votes
0
replies
695
views
RNA-Seq featureCounts Results Annotation File
Nanopore HG38 Rna-Seq Genome
4.2 years ago by santos48 ▴ 40
1
vote
1
reply
1.4k
views
What happens to the genotype field in a g.vcf after CombineGVCFs
GT GATK CombineGVCFs genotype
updated 4.2 years ago by ▴ 20 • written 4.4 years ago by ▴ 420
3
votes
0
replies
953
views
News: Unix / scripting / research computing resource
scripting parallel hpc unix programming
4.2 years ago by bacon4000 ▴ 80
4
votes
9
replies
11k
views
How to find Standard Error (SE) values when not provided in GWAS summary stats?
meta-analysis gwas metal plink Standard error
updated 4.0 years ago by • 0 • written 5.4 years ago by • 0
4
votes
7
replies
2.9k
views
can't run Aracne -- Java error
aracne RNA-Seq network
updated 4.2 years ago by ▴ 740 • written 5.1 years ago by ▴ 750
2
votes
3
replies
1.4k
views
Assembly of three biological replicated metagenomics data
Assembly metagenomics analysis replicate statistics
updated 4.2 years ago by 3.9k • written 4.2 years ago by • 0
4
votes
7
replies
2.7k
views
Should we keep only the uniquely mapped reads for gene expression
RNA-seq
updated 4.2 years ago by ★ 19k • written 4.2 years ago by ▴ 750
0
votes
2
replies
1.7k
views
Plotting residuals for limma lmfit model
linearregression limma normality residuals
4.2 years ago by ritz ▴ 10
0
votes
7
replies
3.1k
views
What are the input files for lwaldron / metaphlanToPhyloseq.R ?
r metagenomics metaphlan
updated 4.2 years ago by • 0 • written 5.1 years ago by ▴ 60
0
votes
1
reply
622
views
blastn for global alignment
global BLAST alignment
updated 4.2 years ago by 153k • written 4.2 years ago by • 0
0
votes
2
replies
725
views
Default number of mismatches in bowtie -v alignment mode?
bowtie
4.2 years ago by lbro • 0
0
votes
3
replies
1.6k
views
samtools depth -r
WGS
4.2 years ago by lz1903 ▴ 10
0
votes
3
replies
1.8k
views
compilation terminated when R package installation in linux without superuser permission
r spp bzlib
4.2 years ago by whaiyu06 ▴ 80
14
votes
4
replies
1.7k
views
How to select columns from a dataframe of which the name ends with a specific word
R
updated 4.2 years ago by 12k • written 4.2 years ago by ▴ 20
2
votes
2
replies
1.2k
views
BWA aln, according to GDC DNA Seq Analysis Pipeline
scores BWA quality GDC Alignment
updated 4.2 years ago by ★ 1.3k • written 4.2 years ago by ▴ 10
2
votes
5
replies
1.8k
views
To retrieve the transcript from gff file with the longest isoform
isoform gff
4.2 years ago by Aneesha • 0
0
votes
2
replies
1.1k
views
Trouble with alignment using STAR - unknown error
RNA-seq alignment STAR
4.2 years ago by foxiw ▴ 10
2
votes
0
replies
790
views
How to integrate two Seurat objects
scRNA-seq Seurat
4.2 years ago by zizigolu ★ 4.4k
0
votes
1
reply
1.1k
views
Circular plot for RNA seq - methylation data
methylome plot rnaseq
updated 4.2 years ago by ★ 3.1k • written 4.2 years ago by ▴ 10
1
vote
2
replies
881
views
How does Belvu calculate conservation scores?
Conservation Belvu
4.2 years ago by jmungar2 ▴ 10
0
votes
0
replies
1.4k
views
PYSCENIC - full garbage collection
PYSCENIC SCENIC GRN CELL SINGLE
4.2 years ago by GiuliaAC ▴ 20
0
votes
0
replies
627
views
How to find allele frequency for a list of eQTLs based on finish/EUR population?
frequency eQTLs allele
4.2 years ago by macsuejacques • 0
0
votes
0
replies
586
views
Genome assembly
illumina bam genome vcf assembly
updated 4.2 years ago by 89k • written 4.2 years ago by • 0
1
vote
1
reply
1.3k
views
How to extract the shortest and the longest isoform from Trinity.fasta file?
assembly fasta trinity
updated 4.2 years ago by 3.9k • written 4.2 years ago by ▴ 20
2
votes
9
replies
5.5k
views
Looping over a function in R, and needing a variable name to save output as unique files
r
updated 4.2 years ago by ▴ 390 • written 4.2 years ago by ▴ 140
1
vote
2
replies
802
views
how to splice a gene sequence
assembly
4.2 years ago by linqide0418 • 0
3
votes
1
reply
1.3k
views
Clarification on KEGG orthologs, why don't all have KEGG modules?
ortholog database kegg
updated 4.2 years ago by 3.9k • written 4.2 years ago by ▴ 750
4
votes
2
replies
1.5k
views
Subread-align: Properly-paired versus not properly paired
alignment subread subread-align RNAseq
4.2 years ago by rependo ▴ 40
2
votes
0
replies
834
views
Herald: The Biostar Herald for Tuesday, June 15, 2021
herald
updated 4.2 years ago by 20 • written 4.3 years ago by 3.6k
2
votes
1
reply
1.6k
views
Molecular docking
pdbqt docking sdf
updated 4.2 years ago by ▴ 940 • written 4.2 years ago by • 0
1
vote
4
replies
1.4k
views
Looking for dataset with scRNA-seq data for normal (non cancer, non iPSCs) but prolifirating cells human (may be mouse or other )
RNA-seq
4.2 years ago by Alexander ▴ 220
1
vote
1
reply
878
views
Interpret PCA as combinations of SNPs
PCA SNPRelate
updated 4.2 years ago by 36k • written 4.2 years ago by • 0
0
votes
1
reply
1.2k
views
Buffer Error with bwa index
hg19 index bwa
updated 4.2 years ago by 166k • written 4.2 years ago by ▴ 250
2
votes
1
reply
1.7k
views
getting a set of coverage/depth metrics for multiple regions
bedtools samtools
updated 4.2 years ago by 36k • written 4.2 years ago by ▴ 20
0
votes
8
replies
2.0k
views
Annotation of 100kb region
Annotation
4.2 years ago by bioinformatics.queries ▴ 70
8
votes
23
replies
5.8k
views
How to get the genes that contain the highest number of isoforms from a fasta file generated by trinity de novo?
assembly fasta trinity
updated 3.7 years ago by • 0 • written 4.2 years ago by ▴ 20
0
votes
3
replies
1.4k
views
Graphic in LEfSe
Graphic
4.2 years ago by pnmb.mbc20 • 0
0
votes
1
reply
1.4k
views
Matplotlib plot stops responding when trying to close it
python python3 ProDy matplotlib
4.2 years ago by Kevin ▴ 70
4
votes
3
replies
2.2k
views
picard MergeBamAlignment fails to merge ubam and bam
picard MergeBamAlignment GATK
4.2 years ago by Frieda ▴ 60
4
votes
5
replies
9.3k
views
6 follow
Where can I find mouse Gene MatriX file format (GMT)?
gene RNA-Seq next-gen
updated 4.2 years ago by ▴ 10 • written 7.7 years ago by ▴ 190
0
votes
0
replies
727
views
Add or make representative diagrams on the axes of a graph with R
graphs ggplot2 data visualization R
4.2 years ago by diego1530 ▴ 80
3
votes
9
replies
2.4k
views
Query regarding WGCNA module
WGCNA R RNA-seq
updated 4.2 years ago by 89k • written 4.2 years ago by ▴ 30
0
votes
2
replies
1.4k
views
TCGA-BRCA download
BRCA TCGA
updated 2.5 years ago by 45k • written 4.2 years ago by ▴ 50
0
votes
0
replies
635
views
Genes in GO pathways
GO pathways
4.2 years ago by some1 ▴ 10
1
vote
2
replies
2.9k
views
annotate VCF file with LRG ?
LRG vcf annotation
updated 3.8 years ago by 45k • written 11.2 years ago by ▴ 600
1
vote
11
replies
3.0k
views
Blast 2.11 not blasting all sequences in a file?
blast
4.2 years ago by DNAngel ▴ 260
0
votes
5
replies
1.4k
views
Dock image for transcriptomics assembly
transcriptomics docker
updated 4.2 years ago by 45k • written 4.2 years ago by ▴ 50
121,898 results • Page 626 of 2438
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Comment: Hifiasm is getting killed while trying to assemble a genome
Comment: How to debug faulty BBmap clumpify command?
Answer: Yeast reference-based genome assembly
Answer: Structural Variant identification on pangenome graphs
Multiple VCF file comparision
Comment: Different UMAP for batch correction in R and Pytho
Answer: Is a direct comparison of the number of up- and down-regulated genes meaningful?
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Recent Replies
Comment: Hifiasm is getting killed while trying to assemble a genome by GenoMax 153k
> I even tried to decrease the number of threads and even used -f0, but nothing is working out. What kind of dataset is this? How many r…
Comment: Hifiasm is getting killed while trying to assemble a genome by Panos ★ 1.8k
How large do you expect the genome to be? For some human genomes that I tried it (i.e. genome size ~3Gbp), peak memory usage was ~160GB RAM…
Comment: How to debug faulty BBmap clumpify command? by marongiu.luigi ▴ 760
Thank you. I am now using the latest version of BBmap and it works. There must have been a file corruption somewhere.
Comment: Yeast reference-based genome assembly by colindaven 7.9k
You're right about contiguity with these exceptionally short ONT reads, but there is no harm in trying. It depends on the repeat content of…
Comment: Transfer harmony-integrated scRNA-seq data to scanpy by Madiha ▴ 10
Hi, I am not sure if you still remmeber the solution you followed that time. But I am stuck with similar problem. scVI is not working good …
Answer: Pipeline for downloading, aligning, and curating influenza A and B sequences for by GenoMax 153k
Have you looked at https://nextstrain.org/ and specifically https://github.com/nextstrain/seasonal-flu Software is available to do the ana…
Comment: Different UMAP for batch correction in R and Pytho by GenoMax 153k
Use this tutorial for how to upload images: https://www.biostars.org/p/309884/#346553 Only difference is instead of using an external imag…
Answer: GTEx sQTL v8 – annotation version used? by GenoMax 153k
If you click over to the `Reference` tab ( https://gtexportal.org/home/downloads/adult-gtex/reference ), it looks like they used GENCODE v.…
Comment: How to Identify Conserved 21-mers Across TE Insertions in Drosophila? by manikin_python9f ▴ 20
Since they are transposons, we don’t know the exact location of them. We know their sequence of insertions from repeatmasker in dm6 genome.…
Comment: Tool 'sra_source' does not exist. by Atefeh • 0
Thanks for your kindness.
Comment: TCGA -derived Large RangeSummarizeExperient file by Tom • 0
It works well. Thank you very much ! @atpoint
Answer: TCGA -derived Large RangeSummarizeExperient file by ATpoint 89k
For the end user these `DFrames` are just regular data.frames, so you can do `col_data[,c("barcode", "patient", "whatever")]` or just do `a…
Comment: magpurify errors by shevch2009 ▴ 20
I have checked with my eyes, and I didn't find it, I have only one contig that starts with k127_458 .... but the name is different - k127_4…
Comment: Yeast reference-based genome assembly by Michael 56k
So, you aren't sure about the exact species? Then you might want to be careful with reference-based assembly in general. I recommend the fo…
Comment: Structural Variant identification on pangenome graphs by Panos ★ 1.8k
That's a very comprehensive list! Thanks for sharing! `minigraph` better suits my needs because all I need is SVs for my genomes. As far a…
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