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1,000 results • Page 3 of 20
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4
votes
4
replies
795
views
Segmentation fault Biopython pairwise alignment
biopython alignment
updated 11 months ago by 21k • written 11 months ago by ▴ 20
4
votes
8
replies
2.0k
views
How to extract promoter sequences from a plant draft genome?
promoter genome
updated 10 months ago by 43k • written 4.6 years ago by ▴ 120
4
votes
6
replies
955
views
Open-Source software. Good or bad for the market?
genomic-analysis software
updated 11 months ago by 43k • written 6.2 years ago by • 0
4
votes
2
replies
562
views
Can I still remove ambient RNA if I do not have raw barcode-gene matrix?
SoupX
6 months ago by malonzm1 ▴ 20
4
votes
2
replies
230
views
Trying to write bwa mem -> samtools view -> samtools sort loop
bwa samtools mapping genome
updated 22 days ago by 161k • written 22 days ago by • 0
4
votes
6
replies
836
views
bwa mem hangs after a few thousand reads
bwa alignment variant-calling bwa-mem
updated 24 days ago by 43k • written 5 months ago by ▴ 30
4
votes
6
replies
2.1k
views
Single nucleotide Polymorphism (SNP)
SNP
updated 10 months ago by 43k • written 9.0 years ago by ▴ 10
4
votes
4
replies
3.3k
views
Unable to install Autogrid4
autogrid software-error autogrid4
updated 11 months ago by 43k • written 3.1 years ago by • 0
4
votes
3
replies
587
views
Identifying enhancers that regulate certain genes
enhancers
updated 9 months ago by ▴ 900 • written 9 months ago by ▴ 40
4
votes
6
replies
2.4k
views
Why weblogo of biopython doesn't work?
Biopython Weblogo
updated 11 months ago by • 0 • written 20 months ago by ▴ 20
4
votes
4
replies
605
views
I cannot install anaconda on ubuntu 22.04
ubuntu anaconda Conda
updated 8 months ago by 43k • written 8 months ago by ▴ 10
4
votes
8
replies
1.2k
views
Error executing nf-core/metaboigniter pipeline
nf-core metaboigniter nextflow
updated 8 months ago by ★ 1.4k • written 8 months ago by • 0
4
votes
16
replies
1.8k
views
How to subset large BAM files specifically/ extract specific subsets?
bamtools RNAseq samtools BAM
updated 9 weeks ago by 43k • written 7 months ago by • 0
4
votes
5
replies
1.2k
views
tranfering sam file easy and fast way
SAM RNA-seq hisat2
updated 8 months ago by 43k • written 2.3 years ago by • 0
4
votes
3
replies
588
views
Over Representation analysis altered pathways in common between comparisons plot
R Visualization DGE ORA
updated 6 months ago by ★ 2.0k • written 6 months ago by ▴ 10
4
votes
7
replies
2.2k
views
About normalization of the datasets from Harmonized TCGA data
protein transcript normalisation
updated 11 weeks ago by 43k • written 21 months ago by ▴ 10
4
votes
4
replies
847
views
retaining only the clusters of interest
seurat single-cell scRna-seq
updated 10 months ago by 43k • written 10 months ago by • 0
4
votes
5
replies
1.1k
views
STAR mapping - regarding output files content
STAR RNA-seq mapping
updated 8 months ago by ▴ 900 • written 8 months ago by • 0
4
votes
7
replies
798
views
Help with weighted nearest neighbor analysis
seurat single-cell
8 months ago by Chris ▴ 260
4
votes
5
replies
538
views
Which refseq_protein db to choose for zingiberaceae
local blastp blast
updated 8 months ago by 141k • written 8 months ago by • 0
4
votes
3
replies
312
views
Getting less DE genes when incorporating all samples
RNA-seq differential-expression deseq2
updated 10 weeks ago by ★ 1.8k • written 10 weeks ago by ▴ 10
4
votes
3
replies
392
views
Single cell analysis of Cancer
cancer single-cell RNA-seq
updated 10 weeks ago by 141k • written 10 weeks ago by ▴ 20
4
votes
3
replies
485
views
Parsing columns with awk
awk
updated 5 months ago by 43k • written 5 months ago by ▴ 300
4
votes
3
replies
727
views
Why is there a big difference between the outputs of `geneBody_coverage` of `RSeQC` when using different bed files?
RSeQC
11 months ago by Dan ▴ 180
4
votes
1
reply
1.7k
views
How does FindNeighbors() and FindClusters() related and work?
seurat clustering
updated 8 months ago by ★ 2.4k • written 8 months ago by ▴ 120
4
votes
4
replies
363
views
Average expression of a sample in single-cell data
single-cell rna-seq
24 days ago by newuser2024 • 0
4
votes
12
replies
3.5k
views
How to read VCF (v4.1) file? (student project) (samtools version 0.1.19)
variant-calling samtools VCF BCF
updated 4 weeks ago by 43k • written 5.5 years ago by ▴ 110
4
votes
5
replies
1.0k
views
VEP run with --af_gnomadg refuses to provide allele frequencies for extremely rare variants
vep gnomad
updated 8 months ago by ▴ 60 • written 8 months ago by 22k
4
votes
11
replies
639
views
Remove X in row name with only number
GSVA
updated 11 weeks ago by 43k • written 11 weeks ago by ▴ 260
4
votes
3
replies
691
views
How to interpret output of PLINK association test (--assoc)
assoc
updated 8 months ago by 11k • written 8 months ago by ▴ 10
4
votes
6
replies
934
views
How to pass from DNA to AA fasta
genetics
updated 11 months ago by ★ 2.4k • written 11 months ago by • 0
4
votes
6
replies
339
views
Protein loops
protein Loop
6 weeks ago by Curious ▴ 10
4
votes
16
replies
960
views
hisat2 location does not exist
hisat2
updated 8 weeks ago by 43k • written 9 weeks ago by • 0
4
votes
14
replies
1.1k
views
remove white space in fastq file
fastq
updated 4 months ago by 141k • written 4 months ago by • 0
4
votes
6
replies
1.0k
views
Python script to automatically read in, name output files & parse R1 & R2 fastq.gz files when given an input directory with raw data files
python fastq
9 months ago by eorr ▴ 30
4
votes
7
replies
554
views
DESeq2 Multifactor Design
RNA-seq DESeq2
updated 13 days ago by 43k • written 14 days ago by ▴ 20
4
votes
6
replies
1.2k
views
Transcript quantification
rna-seq transcriptome SRA
updated 10 months ago by 82k • written 10 months ago by • 0
4
votes
7
replies
2.7k
views
low bootstrap value?
phylogeny genome alignment
updated 11 months ago by 43k • written 4.9 years ago by ▴ 120
4
votes
14
replies
2.7k
views
Is it possible to annotate single genes by snpeff
snp vcf
updated 10 months ago by 43k • written 6.7 years ago by ▴ 70
4
votes
5
replies
1.4k
views
Distributed / parallel computing in bioinformatics
distributed-computing
updated 11 months ago by 43k • written 6.8 years ago by ▴ 750
4
votes
3
replies
306
views
Should you remove PCR duplicates for kmer counting?
kmer dedup duplicates
updated 11 weeks ago by 4.6k • written 11 weeks ago by ▴ 30
4
votes
4
replies
605
views
Request for a linkage analysis tutorial
linkage
updated 8 months ago by 141k • written 8 months ago by ★ 2.9k
4
votes
11
replies
1.8k
views
PCA WITH PLINK
PLINK
updated 8 months ago by 87k • written 8 months ago by • 0
4
votes
8
replies
3.5k
views
How to reduce the number of SNPs for the Lositan software
Lositan SNP
updated 10 months ago by 43k • written 9.5 years ago by • 0
4
votes
8
replies
1.8k
views
Error while running nf-core/rnaseq pipeline
nf-core RNA-seq
11 months ago by eesha28112001 • 0
4
votes
7
replies
812
views
SNP IDs
SNP
5 months ago by kl ▴ 10
4
votes
6
replies
2.6k
views
Convert Nanopore Fast5 files to Fasta format
fast5 fasta Nanopore
11 months ago by Sowmya Pulapet ▴ 70
4
votes
8
replies
1.9k
views
Hello, I have differential ATAC-seq from control and diseased cells (H3K27ac mark as chromatin mark) and wondering how to call enhancers using ROSE …
super-enhancers Enhancers
updated 12 weeks ago by ★ 16k • written 3 months ago by • 0
4
votes
9
replies
573
views
variant calling
variant-calling
updated 23 days ago by 43k • written 24 days ago by • 0
4
votes
7
replies
1.4k
views
.bed files from sequencing platform not containing intervals of "alt", "random" haplotypes. How do I perform coverage and haplotype caller?
exome .bed haplotypes HG38 coverage
updated 9 months ago by 141k • written 9 months ago by • 0
1,000 results • Page 3 of 20
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Recent Replies
Answer: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC: by Mensur Dlakic ★ 27k
They say that we remember better things we figured out on our own, rather than things we were taught. You were literally two clicks away fr…
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https://maayanlab.cloud/clustergrammer/ It's a web-based tool (can also be a python jupyter widget) that I find useful for exploring a pat…
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There is an Agilent array case study in the limma User's Guide, which you might find helpful and somewhat simpler. I don't recommend col…
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The comparison you've done seems exactly right to test whether treatment 2 modifies or enhances the effect of treatment 1. Have you exam…
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There's no need for form a contrast because the score variable is already in the model. A continuous variable is its own contrast. Just run…
Comment: Create a new bed file with all pairwise combinations between two other bed files by J ▴ 10
Oh wow, bedops closest-features, how did I overlook that!! I didn't know about it; thank you! Your awk script is beautiful. This worked per…
Comment: Create a new bed file with all pairwise combinations between two other bed files by J ▴ 10
Thank you Pierre! I'll try this out with my full data set.
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I happend to see one paper doing the similar thing, share it with you guys, "A systematic evaluation of normalization methods and probe rep…
Answer: Create a new bed file with all pairwise combinations between two other bed files by Alex Reynolds 35k
I think Pierre's answer might be correct for your test input, but it doesn't account for the start position of the reference element and so…
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You need to be clear about how `Seurat` defines highly variable genes here. Highly variable genes are the genes that have very high express…
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Please include a link when you are recommending a tool. There can be programs with similar names.
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Check out clustergrammer from Avi Ma'ayan's lab.
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Simple: ```r data <- lapply(files, read_tsv) data <- Reduce(merge, data) # or Reduce(full_join, data) ``` <a href="" title="Text added bec…
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You can make each process use a dedicated environment, see https://www.nextflow.io/docs/latest/conda.html#use-existing-conda-environments …
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Hi, Just thought I'd share this code snippet here for when each file contains multiple samples. I tried using lapply (as suggested by Ram)…
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