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173 results • Page 1 of 4
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38
votes
12
replies
31k
views
9 follow
How to systematically check if a bam file is truncated
Exomeseq
updated 6 days ago by ▴ 170 • written 7.1 years ago by ▴ 240
20
votes
17
replies
13k
views
17 follow
Best Practice On Variant Discovery For Bacteria?
updated 4 hours ago by • 0 • written 11.9 years ago by 33k
7
votes
3
replies
13k
views
Z score in RNAseq
RNA-Seq Zscore
updated 1 day ago by ▴ 60 • written 6.5 years ago by ▴ 310
22
votes
15
replies
10k
views
12 follow
Alternatives To Liftover
liftover genome mapping
updated 1 day ago by • 0 • written 12.5 years ago by ▴ 170
19
votes
10
replies
7.3k
views
7 follow
T2T-CHM13 "complete" human genome gff/gtf annotation file
genomics
written 3.0 years ago by ▴ 590
11
votes
13
replies
6.7k
views
7 follow
log2 fold change in RNA-seq analysis
fold log2 change
updated 20 hours ago by • 0 • written 2.4 years ago by ▴ 10
3
votes
4
replies
6.3k
views
MAUVE: No gene annotations in Genbank file alignments
software-error MAUVE RAST genbank alignment
updated 1 day ago by ▴ 40 • written 9.8 years ago by ▴ 70
13
votes
18
replies
6.2k
views
9 follow
Blastn, need help to increase speed
RNA-Seq blastn blast+
updated 2 days ago by ★ 2.5k • written 3.2 years ago by ▴ 20
5
votes
4
replies
5.1k
views
6 follow
Classic threshold for log2 fold change in RNA-seq experiment
RNA-Seq
updated 1 day ago by • 0 • written 3.9 years ago by ▴ 330
0
votes
7
replies
4.3k
views
B allele frequency (BAF)
snp
updated 6 days ago by ▴ 10 • written 3.7 years ago by ▴ 90
3
votes
7
replies
3.9k
views
Difference in Bismark output methylation call files and coverage files
RRBS Bismark DNA-methylation
updated 20 hours ago by ★ 2.9k • written 3.9 years ago by ▴ 40
8
votes
9
replies
3.0k
views
7 follow
Venter Genome Vcf
vcf
updated 11 hours ago by ▴ 20 • written 10.1 years ago by ▴ 980
7
votes
14
replies
2.9k
views
6 follow
How to find tandem duplications pattern in a DNA sequence
Repeat
updated 4 days ago by ▴ 30 • written 3.1 years ago by • 0
0
votes
3
replies
1.8k
views
Running STRUCTURE from command line
STRUCTURE
updated 2 days ago by 44k • written 3.0 years ago by ▴ 10
1
vote
6
replies
1.5k
views
CellRanger output more cells than specified using --force-cells? Why?
scRNA-seq cellranger
updated 5 days ago by ▴ 30 • written 8 months ago by ▴ 870
2
votes
4
replies
1.2k
views
Is it possible to run CibersortX with a very small number of samples?
cibersortx
1 day ago by Aspire ▴ 330
2
votes
10
replies
1.1k
views
HGVS Nomenclature of Multiple Indels found in Cis
Nomenclature HGVS
updated 3 days ago by 44k • written 5 months ago by 4.2k
4
votes
11
replies
933
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs BED eqtl bedtools
2 days ago by J ▴ 10
1
vote
3
replies
907
views
Which 1000 genomes 30x files should I use for imputation?
1000genomes imputation SNP
updated 1 day ago by • 0 • written 16 months ago by ▴ 160
3
votes
8
replies
868
views
Random Access remote BAM files
htslib BAM
updated 1 day ago by • 0 • written 3 months ago by ▴ 20
1
vote
16
replies
809
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast ncbi
updated 5 days ago by 142k • written 8 days ago by • 0
1
vote
2
replies
733
views
Checking chromosome builds for genotyping data
GWAS Liftover PLINK
updated 5 days ago by • 0 • written 2.6 years ago by • 0
4
votes
9
replies
656
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA R VARIANCE
updated 3 days ago by ▴ 130 • written 8 days ago by ▴ 20
1
vote
10
replies
620
views
Add stats to the plot
R
2 days ago by Ghada • 0
0
votes
2
replies
619
views
minfi::getQC - is default badsamplecutoff of 10.5 always appropriate? ~half of samples fail by this measure
getqc ewas minfi
updated 21 hours ago by • 0 • written 10 months ago by • 0
0
votes
1
reply
610
views
Illumina methylation EPIC V2 array
ewas methylation enrichment missMethyl EPIC
updated 3 days ago by ▴ 40 • written 8 months ago by • 0
2
votes
7
replies
602
views
KEGG analysis in R
KEGG clusterProfiler Zea-mays
updated 2 days ago by • 0 • written 6 weeks ago by ▴ 90
1
vote
3
replies
558
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics bootstrap
updated 3 days ago by ▴ 160 • written 6 weeks ago by ▴ 40
0
votes
8
replies
548
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp vcf genomics plink
updated 4 days ago by 162k • written 13 days ago by • 0
0
votes
9
replies
536
views
ComplexHeatmap - How to change fontsize of rowAnnotation
r ComplexHeatmap
updated 4 hours ago by 11k • written 6 days ago by • 0
4
votes
9
replies
528
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch alignment
6 days ago by Gabriel R. ★ 2.9k
1
vote
8
replies
501
views
Overlapping Ranges within Granges object
Genomicranges IRanges GRanges
updated 6 days ago by 35k • written 10 days ago by ▴ 60
3
votes
5
replies
474
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome PHG graph
2 days ago by beantkapoor16 ▴ 10
3
votes
5
replies
441
views
Super ehancers
enhancers
updated 2 days ago by ★ 17k • written 22 days ago by • 0
1
vote
5
replies
401
views
Reconstruction of locus, order contigs
contigs cluster alignment locus
updated 6 days ago by ★ 2.0k • written 7 days ago by • 0
1
vote
4
replies
392
views
some error in building kraken2 database
metagenome kraken2
updated 23 hours ago by 142k • written 4 weeks ago by • 0
6
votes
4
replies
387
views
Details on salmon index
Salmon
updated 6 days ago by 6.6k • written 8 days ago by • 0
1
vote
2
replies
386
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx cibersort error RNA-Seq deconvolution
updated 2 days ago by • 0 • written 3 months ago by ▴ 10
0
votes
4
replies
379
views
How to handle duplicated genes in TCGA data?
TCGA GDC mRNA
updated 6 days ago by ▴ 130 • written 7 days ago by • 0
1
vote
6
replies
369
views
What marks a De-Novo Genome assembly as FAILED?
nanopore denovo illumina assembly genome
3 days ago by Umer ▴ 50
0
votes
4
replies
367
views
how to treat the replicates while performing WGCNA
clustering WGCNA replicates
15 hours ago by mavy ▴ 10
3
votes
4
replies
362
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq patch freeze genome
updated 6 days ago by 22k • written 8 days ago by • 0
1
vote
2
replies
359
views
is there a tool to recover corrupted fastq files
fastq short-read
updated 4 days ago by • 0 • written 3 months ago by ▴ 60
1
vote
4
replies
355
views
Help with Biopython for Beginner
Python ORF FASTA Biopython
updated 6 days ago by 21k • written 15 days ago by • 0
0
votes
4
replies
351
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
rna-seq
4 days ago by Bibi • 0
2
votes
3
replies
350
views
Trimming tool
Trimming
updated 3 days ago by 44k • written 6 days ago by • 0
2
votes
4
replies
337
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell ambient-RNA
updated 1 hour ago by ★ 1.6k • written 7 days ago by ▴ 130
0
votes
2
replies
338
views
transanno liftvcf "Error: length of chromosome [chr] is not equal to length in chain file. Are you using correct reference?"
liftover transanno
2 days ago by ezz3 • 0
4
votes
6
replies
333
views
Mouse or Rat Gene Expression Data Similar to GTEx
whole-body expression atlas
16 hours ago by Shicheng Guo ★ 9.4k
0
votes
2
replies
331
views
Design for complex RNA-Seq experiment using Deseq2
Model.Matrix RNA-Seq Limma DESeq2 edgeR
4 days ago by Ezequiel • 0
173 results • Page 1 of 4
Recent Votes
Answer: plink2 cannot make bed file
Answer: plink2 cannot make bed file
Answer: Conda, bioconda, anaconda, are they different?
Answer: Conda, bioconda, anaconda, are they different?
Gene Set Enrichment Analysis
Comment: Unexpected read length from NGS
Answer: Unexpected read length from NGS
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Comment: How to scrape BioMart data from https://sorfs.ugent.be/ website by Pierre Lindenbaum 162k
did you ask the authors to restore their server ?
Comment: Single cell analysis: Unable to subset cells in seurat object using desired nFea by sc_analysis • 0
Yes. But after applying: merged_seurat_objects_filtered <- subset(x = merged_seurat_objects, subset = nFeature_RNA > 200 & nFeature_RNA < …
Comment: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction by fracarb8 ★ 1.6k
This [paper][1] provides a comparison of the three methods in different settings. [1]: https://genomebiology.biomedcentral.com/articles…
Comment: Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files by Deepthi • 0
pop up with sam error . Error reading _rstarts[] array: 21720, 23124
Comment: Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files by ATpoint 82k
See me edit I just made for the fastq check.
Comment: Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files by Deepthi • 0
Thanks will check and update here.
Answer: Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files by ATpoint 82k
bowtie -x idx file.fastq | samtools view -o out.bam You might be messing up things with these positional arguments. Use this above. Us…
Comment: Annotating single cell data automatically by Francesco ▴ 10
- In order to run Azimuth: ``` AzimuthClusters <- RunAzimuth(seurat_obj, reference = "pbmcref") ``` - singleR ``` surveyRefere…
Comment: Single cell analysis: Unable to subset cells in seurat object using desired nFea by fracarb8 ★ 1.6k
You are not subsetting based on `nFeature`. You are subsetting based on `nFeature` **AND** `nCount` **AND** `perc mt`.
Answer: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction by txema.heredia ▴ 130
Update: I ran CellBender on these samples and compared its results with SoupX and DecontX. vs SoupX: ![cellbender vs SoupX][1] …
Comment: Unexpected read length from NGS by QX • 0
thank you all!
Comment: How to calculate nucleotide diversity (mtDNA, PacBio_data), Suggest me some tool by hashim.rana11 ▴ 20
Initially, I tried using Samtools and BCFtools, followed by running a script in Python (PyCharm) to measure nucleotide diversity![nucleoti…
Comment: Best Practice On Variant Discovery For Bacteria? by Ruqaiya • 0
I used HaploTypecaller but my plasmid reads are not present in the output vcf file ... but it's there in my input file
Answer: How to calculate nucleotide diversity (mtDNA, PacBio_data), Suggest me some tool by Michael 54k
Variants should be called using a specialized mitochondrial variant caller, e.g.: [GATK Mutect2 CallMt][1] Then, pi, Tajima's D, and oth…
Comment: Splitting query fasta file for Diamond Blastp make the process faster? by kmat • 0
I used `seqkit split` to divide the query FASTA file into 10 parts and then ran `diamond blastp` on each file using 44 threads. The process…
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