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774 results • Page
1 of 16
Sort: Votes
Rank
Views
Votes
Replies
298
votes
122
replies
28k
views
29 follow
Mean Length Of Fasta Sequences
code
fasta
sequence
codegolf
updated 21 days ago by
jena
▴ 270 • written 13.2 years ago by
Eric Normandeau
11k
170
votes
41
replies
91k
views
27 follow
Multiline Fasta To Single Line Fasta
fasta
updated 3 days ago by
Ram
40k • written 12.3 years ago by
Palu
▴ 250
162
votes
64
replies
80k
views
39 follow
Selecting Random Pairs From Fastq?
random
fastq
illumina
sequence
updated 6 days ago by
rohitsatyam102
▴ 750 • written 12.5 years ago by
Ketil
4.1k
146
votes
70
replies
46k
views
20 follow
Tutorial:
Network plot from expression data in R using igraph
microarray
RNA-Seq
R
network
updated 28 days ago by
Raheleh
▴ 260 • written 5.8 years ago by
Kevin Blighe
86k
124
votes
13
replies
165k
views
13 follow
How Can I Convert Bam To Sam?
bam
next-gen-sequencing
sam
updated 20 days ago by
Ram
40k • written 13.2 years ago by
Biomed
4.9k
105
votes
26
replies
40k
views
23 follow
How To Create Mutation Diagram In R Or In Any Tools?
mutation
domain
r
updated 7 days ago by
zx8754
11k • written 10.7 years ago by
henryvuong
▴ 810
100
votes
38
replies
29k
views
34 follow
Forum:
List of cloud genomics companies
cloud-genomics
updated 26 days ago by
Jeremy Leipzig
21k • written 9.9 years ago by
14134125465346445
★ 3.6k
81
votes
21
replies
40k
views
15 follow
How To Get Bed File Containing Exons Of Canonical Transcripts And Their Corresponding Gene Symbols
bed
transcript
ucsc
biomart
updated 11 days ago by
Joel Wallenius
▴ 180 • written 9.6 years ago by
pristanna
▴ 750
75
votes
18
replies
2.1k
views
11 follow
Blog:
A list of technical advantages of Snakemake over Nextflow | Cloud solution for Snakemake
Snakemake
updated 7 days ago by
Ram
40k • written 11 days ago by
Kenny
▴ 30
60
votes
21
replies
2.9k
views
14 follow
Reproduce the article "The complete sequence of a human genome."
genome
assembly
updated 24 days ago by
Michael
53k • written 26 days ago by
sqshigg
▴ 60
38
votes
25
replies
8.1k
views
13 follow
FASTA file of fixed length
sequence
fasta
updated 13 days ago by
Ram
40k • written 7.5 years ago by
waqasnayab
▴ 250
36
votes
5
replies
5.8k
views
Tutorial:
[Beginner] Introduction to bioinformatics file types
fastq
fasta
bed
SAM
updated 18 days ago by
gallardodiazmiriam
▴ 20 • written 8.2 years ago by
Luke Crichton
▴ 410
36
votes
16
replies
28k
views
14 follow
Generating consensus sequence from bam file
genome
samtools
bwa
fasta
updated 6 days ago by
jkbonfield
★ 1.1k • written 4.6 years ago by
chparada
▴ 60
35
votes
23
replies
27k
views
11 follow
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
bcftools
updated 24 days ago by
s.w.vanderlaan
▴ 40 • written 2.2 years ago by
Michal Nevo
▴ 110
33
votes
23
replies
18k
views
12 follow
Is there a tool that sorts gtf files?
RNA-Seq
genome
updated 12 days ago by
alejandrogzi
▴ 30 • written 5.5 years ago by
JJ
▴ 660
23
votes
12
replies
1.9k
views
Genes encoded on both strands of DNA?
Genes
strand
updated 4 days ago by
Ram
40k • written 17 months ago by
A_heath
▴ 140
21
votes
9
replies
21k
views
9 follow
Building Snpeff Database
vcftools
snp
gatk
updated 20 days ago by
Ram
40k • written 11.1 years ago by
bioinfo
▴ 830
19
votes
10
replies
860
views
Forum:
Pain points using commercial clouds
gpt
tinybio
updated 10 days ago by
vincenthus
▴ 70 • written 26 days ago by
Sasha
▴ 720
19
votes
10
replies
29k
views
6 follow
read depth using samtools
depth
samtools
updated 11 days ago by
Sachin
• 0 • written 4.7 years ago by
LimMo
▴ 30
19
votes
14
replies
859
views
Forum:
What is the amount of sequencing data produced annually?
data
research
sequencing
updated 5 days ago by
Jeremy Leipzig
21k • written 6 days ago by
vincenthus
▴ 70
18
votes
22
replies
8.1k
views
10 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
annotation
updated 3 days ago by
evoecogen
▴ 20 • written 3.8 years ago by
Juke34
8.2k
18
votes
10
replies
14k
views
Could you please explain Fold change, % of change, and log2 fold change (L2FC) to a layment?
gene
RNA-Seq
next-gen
fold-change
updated 10 days ago by
Ram
40k • written 3.9 years ago by
WUSCHEL
▴ 720
16
votes
16
replies
1.8k
views
Species identifcation using 16s rRNA
16srRNA
fasta
updated 4 days ago by
Ram
40k • written 2.6 years ago by
A_heath
▴ 140
13
votes
13
replies
6.5k
views
6 follow
Extract SNPs flanking sequences based on VCF and genome Fasta files
snp
sequence
genome
updated 27 days ago by
LauGuillardin
• 0 • written 5.1 years ago by
Denis
▴ 280
13
votes
10
replies
598
views
8 follow
scRNAseq Differential expression analysis
scRNA-seq
Differential-Expression
Seurat
updated 1 day ago by
ATpoint
76k • written 3 days ago by
MVJ
▴ 10
13
votes
5
replies
966
views
Annotating TSS: By Transcript or by Gene? Code Validation Help Needed!
genome
bed
transcript
TSS
updated 9 days ago by
i.sudbery
17k • written 4 months ago by
Rafael Soler
★ 1.2k
12
votes
5
replies
13k
views
How to combine chromosome vcf files
Assembly
alignment
next-gen
genome
updated 25 days ago by
Pierre Lindenbaum
157k • written 5.3 years ago by
williamsbrian5064
▴ 480
11
votes
7
replies
3.4k
views
7 follow
Assembler for only nanopore data
genomics
Assembly
ONT
Abyss
updated 14 days ago by
GenoMax
134k • written 4.4 years ago by
ringourquia
▴ 20
11
votes
4
replies
907
views
How to determine % similarity between genomes?
mauve
mugsy
genome-alignment
updated 4 days ago by
Ram
40k • written 2.5 years ago by
A_heath
▴ 140
11
votes
8
replies
761
views
6 follow
Forum:
How to write a review article in bioinformatics
article
review
updated 25 days ago by
Ram
40k • written 6 weeks ago by
joey
▴ 10
10
votes
13
replies
12k
views
6 follow
How to annotate only selected genes on a heatmap
R
updated 21 days ago by
GenoMax
134k • written 6.3 years ago by
h.fushimi.x689
▴ 30
10
votes
8
replies
11k
views
8 follow
How to install gdc-client in Ubnutu
ubuntu
gdc-client
updated 14 days ago by
Ram
40k • written 7.1 years ago by
pxf109
▴ 20
10
votes
9
replies
1.1k
views
Help interpretating DESeq2 output
Deseq2
Fold-Change
RNA-seq
updated 10 days ago by
Ram
40k • written 2.8 years ago by
nanoide
▴ 100
10
votes
18
replies
3.1k
views
how to identify CDR region in antibody sequence
CDR
antibody
updated 25 days ago by
Ram
40k • written 15 months ago by
reany
▴ 50
10
votes
11
replies
1.2k
views
Seeking feedback on ChIP-seq normalization method: Calculating scaling factors by dividing input by IP, including spike-in
coverage
spike-in
scaling-factor
ChIP-seq
17 days ago by
kalavattam
▴ 180
10
votes
5
replies
25k
views
FastQC with multiple FASTQ files
ngs
fastqc
multiple
updated 7 days ago by
Ram
40k • written 5.3 years ago by
m98
▴ 400
10
votes
8
replies
560
views
Adding a control sample to bulk RNA-seq
RNA-seq
4 days ago by
Chris
▴ 180
9
votes
12
replies
4.2k
views
converting a list of genes and interaction to a graph
gene
R
updated 5 days ago by
Amirhossein Hajianpour
▴ 40 • written 7.7 years ago by
fi1d18
★ 4.2k
9
votes
3
replies
407
views
Seeking a real project
thesis
project
updated 12 days ago by
Ram
40k • written 14 days ago by
m.ranjbar2009
▴ 20
9
votes
7
replies
6.7k
views
Gc Content From Bam
gc
bam
awk
perl
updated 24 days ago by
Ram
40k • written 9.6 years ago by
filipzembol
▴ 170
9
votes
5
replies
4.2k
views
CWL: how to set default values
Common-Workflow-Language
cwl
updated 14 days ago by
Ram
40k • written 6.9 years ago by
bird77
▴ 80
9
votes
8
replies
3.5k
views
bcftools multiallelic split not working
bcftools
vcf
updated 24 days ago by
DareDevil
★ 3.3k • written 2.1 years ago by
from the mountains
▴ 220
9
votes
4
replies
1.2k
views
How to extend contigs from single-end reads?
contigs
contig-extension
updated 4 days ago by
Ram
40k • written 3.0 years ago by
A_heath
▴ 140
9
votes
5
replies
7.0k
views
Genomic Bam To Transcriptome Bam
bam
samtools
updated 6 days ago by
Ram
40k • written 9.8 years ago by
dfernan
▴ 750
9
votes
8
replies
5.2k
views
7 follow
CONTRA for CNV detection. troubleshooting
genome
next-gen
cnv
software-error
sequencing
updated 24 days ago by
Avinash
• 0 • written 9.3 years ago by
Kizuna
▴ 860
9
votes
6
replies
1.3k
views
6 follow
Forum:
GTF files from Ensembl Releases 105 and 106 unsorted
Ensembl
bug
GTF
updated 13 days ago by
ATpoint
76k • written 10 months ago by
dlaehnemann
▴ 30
9
votes
4
replies
1.1k
views
Illumina Q score
Illumina
quality-score
updated 4 days ago by
Ram
40k • written 2.0 years ago by
A_heath
▴ 140
8
votes
14
replies
1.8k
views
How to remove fasta headers in a multifasta file and write file name as a fasta header?
gene
sequence
genome
alignment
next-gen
updated 17 days ago by
Joe
21k • written 3.0 years ago by
Kumar
▴ 120
8
votes
2
replies
2.9k
views
How to edit fasta headers to keep only ID and organism?
fasta
updated 4 days ago by
Ram
40k • written 3.0 years ago by
A_heath
▴ 140
8
votes
7
replies
1.2k
views
Whole genome species clustering
phylogeny
assembly
phylogenetics
updated 27 days ago by
pmiller
• 0 • written 2.4 years ago by
robert.murphy
▴ 80
774 results • Page
1 of 16
Recent Votes
How to identify 16s sequences from binning data(contigs)?
geom_signif() uses t-test to compare between more than 3 groups... Isn't this wrong?
Answer: Filter transcription factors
Comment: Calculation of TMB on gene level
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool?
Comment: ATAC-seq troubleshoot - Just Noise
t2t human reference genome for RNA-seq
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Comment: Violin plot (Monocle 3) - Troubleshooting
by
fracarb8
★ 1.2k
You did not add the screenshot.
Answer: BED files
by
Alex Reynolds
35k
Generically via `bedmap`: ``` bedmap --echo --echo-map --count exome.bed annotations.bed > answer.bed ``` The `annotations.bed` fil…
Comment: geom_signif() uses t-test to compare between more than 3 groups... Isn't this wr
by
dariober
14k
It seems to me that anova followed by HSD is a more sensible approach than applying independent t-tests. Granted this is the first time I s…
Comment: BED files
by
barslmn
★ 1.8k
I am guessing you want the annotation files. https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/
Comment: Filter human transcription factors
by
Alex Reynolds
35k
Curious how redundant these TFs are. Jeff Vierstra has done some analysis on this to simplify model sets: https://www.vierstra.org/resource…
Comment: Read block operation failed with BAM file
by
Alex Reynolds
35k
https://github.com/samtools/htslib/pull/1676 patches a seek issue in `htslib` (upon which `samtools` and `pysam` depend)
Comment: Merging the filename with tsv files for master file
by
barslmn
★ 1.8k
Could you add samples from your files and your expected output.
Comment: Download an example of fully-imputed VCF files ?
by
barslmn
★ 1.8k
Check out the 1000 genomes project. https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/
Comment: obtaining circular RNAs' sequences from circBase
by
Barry Digby
★ 1.2k
Sorry my mistake! it’s been a minute since I’ve used these sites. Yes that it is common place, what is the goal of your analysis using th…
Comment: gene correlations in between two groups
by
ATpoint
76k
Use specialized software to analyse CRISPR/RNAi data, such as MAGeCK.
Comment: gene correlations in between two groups
by
edus_bioinfo
▴ 40
To be more clear, I have RNAi data from depmap with different cell lines and I separated them into two groups according to their EGFR mutat…
Comment: ATAC-seq troubleshoot - Just Noise
by
ATpoint
76k
You have reads, so sequencing is obviously fine. This is how the banding should look: https://kb.10xgenomics.com/hc/article_attachments/360…
Comment: Program for Overlapping DMRs (Differentially Methylated Regions) Between Groups
by
Basti
★ 1.7k
Do not use excel for bioinformatics purposes, using R you could use GRanges objects to find overlaps between your regions : https://www.bio…
Answer: Saving the output of LD pruning from SNPRelate package as a new GDS file
by
Patrick
• 0
Thank you James for the response; My problem is only if I want to use the output of LD pruning in a different software, like STRUCTURE (to …
Answer: Average Coverage after Assembly (Spades)
by
taniapsduarte
• 0
Hi, I'm running into the same issue. Did you make it work? Or did you find an alternative method? Thanks!
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