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1,000 results • Page 2 of 20
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5
votes
3
replies
664
views
Strand bias in supplementary alignments from Nanopore
minimap2 nanopore strand
updated 6 months ago by ★ 3.8k • written 6 months ago by 14k
5
votes
7
replies
877
views
About the value in bigwig file
ATAC-seq
updated 10 months ago by ▴ 900 • written 10 months ago by ▴ 280
5
votes
6
replies
851
views
Calculate the percentage of genomic region covered from the BED file.
NGS sequencing genomics exome genes
updated 9 months ago by ▴ 900 • written 9 months ago by ▴ 40
5
votes
6
replies
1.8k
views
Filter out Bam not overlapping with Bed File (keeping a read and its mate)?
samtools bam bed
updated 11 months ago by 44k • written 18 months ago by ▴ 350
5
votes
5
replies
2.5k
views
Quickly retrieve reference genome sequence within python
sequence python
updated 6 months ago by ▴ 20 • written 5.6 years ago by ▴ 20
5
votes
1
reply
1.9k
views
How does FindNeighbors() and FindClusters() related and work?
seurat clustering
updated 9 months ago by ★ 2.5k • written 9 months ago by ▴ 120
5
votes
8
replies
3.7k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression RNA-seq gene-ontology
updated 5 weeks ago by 44k • written 6.6 years ago by ★ 1.6k
5
votes
8
replies
1.1k
views
sc-RNA seq pipeline
scRNA-seq NGS RNA-Seq
4 months ago by Researcher ▴ 30
5
votes
5
replies
670
views
Counting 705 fasta header characters ('>') in human genome
human-genome genetics
updated 7 months ago by 82k • written 7 months ago by ▴ 10
5
votes
3
replies
1.0k
views
abyss-pe genome assembly
konnector abyss-pe
updated 11 months ago by 44k • written 5.3 years ago by • 0
5
votes
5
replies
680
views
Normalization and Genome-Wide Comparisons with Chipseq
chip-seq Chipseq Normalization
updated 5 months ago by ▴ 500 • written 5 months ago by ▴ 10
5
votes
10
replies
883
views
Error when viewing a bam file
samtools
updated 11 months ago by 44k • written 12 months ago by ▴ 280
5
votes
3
replies
564
views
Visualisation of accessible regions in single cell atacseq data
visualization scATAC-seq single-cell
updated 8 months ago by 44k • written 8 months ago by ▴ 100
5
votes
8
replies
2.0k
views
looking for tools to detect RNA contamination in DNA
RNA-Seq DNA-Seq contamination QC
updated 7 months ago by • 0 • written 3.8 years ago by ▴ 230
5
votes
1
reply
693
views
Learning Linux advance commands
grep awk linux sed
updated 7 months ago by ▴ 60 • written 19 months ago by ▴ 140
5
votes
7
replies
993
views
Salmon index not progressing
salmon
updated 8 months ago by 54k • written 8 months ago by ▴ 160
5
votes
10
replies
1.3k
views
the distribution of log2Fc and t value are not similar for bulk RNA-seq
decoupleR RNA-seq
9 months ago by alwayshope ▴ 40
5
votes
5
replies
7.3k
views
Converting scRNA-Seq to Bulk-RNASeq
scRNASeq bulk-RNASeq RNA-Seq single-cell
updated 5 weeks ago by • 0 • written 3.9 years ago by ★ 1.8k
5
votes
8
replies
669
views
Multiple threads on ubuntu server
Ubuntu
updated 4 months ago by 6.4k • written 4 months ago by ▴ 50
5
votes
35
replies
3.8k
views
Reduce set of chromosomes in Pangenome graph
pangenome vg
updated 10 months ago by ▴ 460 • written 11 months ago by • 0
5
votes
2
replies
1.8k
views
Batch effects from sequencing samples accross multiple flow cells.
rna-seq batch batch-effect sequencing
updated 4 weeks ago by 44k • written 3.0 years ago by ▴ 60
5
votes
1
reply
704
views
Challenges in Variant Calling and Genotyping with Short-Read Data Mapped to a Pangenome Graph: Seeking Guidance
vg pggb giraffe
updated 7 months ago by ▴ 460 • written 7 months ago by ▴ 30
5
votes
7
replies
534
views
RNA seq analysis
DESeq RNA-seq
6 days ago by Jacek ▴ 20
5
votes
8
replies
2.5k
views
SV calling using giraffe/vg
vg Giraffe calling structural variant
updated 10 months ago by ▴ 460 • written 16 months ago by • 0
5
votes
4
replies
749
views
FASTQ to BAM to CRAM to FASTQ
Samtools
6 months ago by ManuelDB ▴ 80
5
votes
6
replies
1.4k
views
DESeqDataSetFromHTSeqCount function taking long time and utilizing more RAM
DESeq2 R RNA-Seq
updated 11 months ago by 44k • written 4.1 years ago by ▴ 90
5
votes
6
replies
464
views
7 follow
Seeking Help with Unexpected MA Plot Output
MAplot RNAseq Rstudio
updated 7 weeks ago by 100k • written 7 weeks ago by • 0
5
votes
11
replies
1.4k
views
Interpret IGV output inversion
variant-calling IGV alignment
updated 9 months ago by ★ 3.8k • written 9 months ago by ▴ 300
5
votes
5
replies
609
views
Generate BED file
bed
3 months ago by daffodil ▴ 10
5
votes
5
replies
354
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
13 days ago by Chris ▴ 280
5
votes
1
reply
651
views
Enricher with Gene Symbols
DGE ClusterProfiler Enrich ORA
updated 9 months ago by ★ 2.5k • written 9 months ago by ▴ 100
5
votes
7
replies
2.7k
views
DESeq2 for differential gene expression on GTEx dataset
differential-gene-expression RNA-Seq GTex DESeq2
updated 5 weeks ago by 44k • written 6.5 years ago by ▴ 10
5
votes
5
replies
565
views
Example MAF Files
MAF
updated 5 months ago by 44k • written 5 months ago by ▴ 120
5
votes
4
replies
1.7k
views
Detection of DE genes among different tissues of an organism during time - RNA seq
detection DE-genes multi-treatments time-series
updated 11 months ago by 44k • written 7.8 years ago by ▴ 760
5
votes
7
replies
3.2k
views
8 follow
bwa mem -T (alignment score) not doing anything
SNP genome sequence
updated 7 months ago by 100k • written 5.9 years ago by ▴ 10
5
votes
3
replies
444
views
samtools view: error reading file
samtools bowtie2
updated 10 weeks ago by ▴ 70 • written 11 weeks ago by • 0
5
votes
2
replies
959
views
Recommended way to normalize SmartSeq2 gene expression matrix to better match 10X expression data
rna-seq smartseq2 r
updated 7 months ago by ▴ 70 • written 8 months ago by ▴ 10
5
votes
11
replies
1.0k
views
Make heatmap for RNA-seq with non replicate
RNA-seq
updated 9 months ago by 44k • written 9 months ago by ▴ 280
5
votes
4
replies
1.2k
views
Converting Bam file to Fasta (Zipped)
bedtools samtools
updated 11 months ago by 44k • written 19 months ago by ▴ 350
4
votes
6
replies
2.2k
views
Single nucleotide Polymorphism (SNP)
SNP
updated 10 months ago by 44k • written 9.1 years ago by ▴ 10
4
votes
1
reply
663
views
How to interpret Clustree results?
scRNA clustering clustree
updated 9 months ago by 3.9k • written 9 months ago by ▴ 120
4
votes
3
replies
617
views
Identifying enhancers that regulate certain genes
enhancers
updated 10 months ago by ▴ 900 • written 10 months ago by ▴ 40
4
votes
8
replies
1.9k
views
Error while running nf-core/rnaseq pipeline
nf-core RNA-seq
12 months ago by eesha28112001 • 0
4
votes
12
replies
7.9k
views
6 follow
BWA error: no ID within the read group line
bwa readgroups RG parallel
updated 3 months ago by ▴ 10 • written 3.4 years ago by ▴ 60
4
votes
4
replies
829
views
Segmentation fault Biopython pairwise alignment
biopython alignment
updated 11 months ago by 21k • written 12 months ago by ▴ 20
4
votes
14
replies
1.2k
views
remove white space in fastq file
fastq
updated 5 months ago by 142k • written 5 months ago by • 0
4
votes
2
replies
697
views
Visualization package for Maf Files using Python
Python maftools Visualization MAF
updated 7 months ago by ★ 1.5k • written 7 months ago by ▴ 100
4
votes
16
replies
1.1k
views
hisat2 location does not exist
hisat2
updated 12 weeks ago by 44k • written 3 months ago by • 0
4
votes
3
replies
632
views
Over Representation analysis altered pathways in common between comparisons plot
R Visualization DGE ORA
updated 7 months ago by ★ 2.0k • written 7 months ago by ▴ 10
4
votes
7
replies
798
views
Alternative for grep in a for loop
linux
updated 7 months ago by 44k • written 7 months ago by ▴ 20
1,000 results • Page 2 of 20
Recent Votes
Answer: converting transcript IDs (Ensembl) to gene symbols in R
Comment: Trimming tool
Answer: Trimming tool
Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
Comment: Practical Haplotype Graph v2 not finding correct paths
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Recent Replies
Answer: z-score of gene set by Matthias Zepper 4.6k
The z-score is a measure of how many standard deviations a particular data point is from the mean of a distribution. A positive z-score ind…
Answer: converting transcript IDs (Ensembl) to gene symbols in R by bk11 ★ 2.5k
You can do as following: library(biomaRt) # Set up the Ensembl BioMart connection ensembl <- useEnsembl(biomart = "genes",…
Comment: How can we convert a vcf to fasta, so that I can blast some genes against that w by Pierre Lindenbaum 161k
well you try to use FastaAlternateReferenceMaker https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateReferenceMak…
Comment: z-score of gene set by bk11 ★ 2.5k
Can you please tell us what will be your propose of z-score calculation?
Comment: DRAGEN gVCF files and joint calling GATK-GenomicsDB by DBScan ▴ 300
I think I did it once, but why would you use GATK with DRAGEN gVCF files? If you have a DRAGEN, the iterative gVCF Genotyper does a much fa…
Answer: Practical Haplotype Graph v2 not finding correct paths by beantkapoor16 ▴ 10
So, I just tested it and it's performing much better now. Most of the haplotype paths are coming from the expected haplotypes (australasica…
Comment: Kraken2 Custom Database non-deterministic results by Bjorn • 0
Thank you!
Comment: Generating a Bed file from a Fasta file by Pierre Lindenbaum 161k
there is not enough information. you have to show us the command you used, a snapshot of your fasta...
Comment: Practical Haplotype Graph v2 not finding correct paths by beantkapoor16 ▴ 10
That's great. I will test it and let you know how it goes. Thank you.
Comment: Generating a Bed file from a Fasta file by pirku • 0
I tried running BLAT, but the output looks like this. Seems like none of the sequences were mapped/aligned match mis- rep. N's Q gap…
Comment: Where to find old version of GATK best practice by GenoMax 142k
You could try and look up a snapshot of the page(s) - https://web.archive.org/ Which specific best practice are you referring to? https:/…
Comment: Generating a Bed file from a Fasta file by Pierre Lindenbaum 161k
you could run blast or any other aligner to get the coordinate(s) of your fasta on a reference genome.
Answer: Running STRUCTURE from command line by Arthur • 0
If it cans help, I got the same error message : There were errors in the input file (listed above). According to "mainparams" the inp…
Comment: CreateSeuratObject taking very long by Nitin Narwade ★ 1.6k
I am not sure whether it will speedup the conversion but you can give it a try. convert your dataframe into a sparse matrix before creatin…
Comment: Practical Haplotype Graph v2 not finding correct paths by pjb39 ▴ 220
The timing for your question is excellent. The fix was released yesterday.
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