Notable Question - Badge - Bioinformatics Stack Exchange

Notable Question

Question with 2,500 views. This badge can be awarded multiple times.

Awarded 336 times.

bigWig to bed for regions above/below threshold

Awarded Nov 25 at 11:43

isthisthat

331 silver badge4 bronze badges

how to have a blast xml file in a readable and understandable way

Awarded Nov 19 at 12:41

serpipanton

211 silver badge2 bronze badges

how is the DNA Integrity Number (DIN) calculated in Bioanalyzer/TapeStation?

Awarded Nov 8 at 15:10

719016

2,32413 silver badges19 bronze badges

10X low rate of correct barcodes was observed for the candidate chemistry choices for the input

Awarded Nov 7 at 17:37

ciwei

411 silver badge5 bronze badges

bedtool intersect multiple bed files

Awarded Nov 1 at 23:34

kcm

1,77412 silver badges27 bronze badges

Perplexity is too large

Awarded Oct 31 at 8:51

Nikita Vlasenko

2,5383 gold badges24 silver badges37 bronze badges

How to Sort and Index a SAM file without converting it to BAM?

Awarded Oct 26 at 13:20

alec_djinn

1031 silver badge3 bronze badges

Samtools sort: most efficient memory and thread settings for many samples on a cluster

Awarded Oct 25 at 21:50

Mark Ebbert

1,30410 silver badges20 bronze badges

10X Illumina demultiplexing sample sheet issue

Awarded Oct 25 at 12:08

Nikita Vlasenko

2,5383 gold badges24 silver badges37 bronze badges

Visualizing FindMarkers result in Seurat using Heatmap

Awarded Oct 25 at 0:25

Dahlia

31 silver badge5 bronze badges

How do I carry out an ancestry/admixture test on a single VCF file?

Awarded Oct 24 at 3:10

gringer♦

13.8k5 gold badges23 silver badges79 bronze badges

Strange per sequence GC content results

Awarded Oct 23 at 10:41

beginner

6317 silver badges15 bronze badges

Splitting fasta file into smaller files based on header pattern

Awarded Oct 20 at 2:58

kcm

1,77412 silver badges27 bronze badges

10X cellranger count, [error] The chemistry was unable to be automatically determined

Awarded Oct 16 at 20:18

Nikita Vlasenko

2,5383 gold badges24 silver badges37 bronze badges

How to sort legends alphabetically in plotly dash with category_orders function

Awarded Oct 16 at 15:40

Riya

3072 silver badges8 bronze badges

Why do some assemblers require an odd-length kmer for the construction of de Bruijn graphs?

Awarded Oct 12 at 19:42

Kamil S Jaron

5,5171 gold badge24 silver badges59 bronze badges

How can I easily get the read size distribution of reads mapping on a certain set of regions?

Awarded Sep 30 at 2:17

bli

3,1001 gold badge14 silver badges36 bronze badges

Seurat: Error in FetchData.Seurat(object = object, vars = unique(x = expr.char[vars.use]), : None of the requested variables were found:

Awarded Sep 19 at 8:11

Joy

211 silver badge2 bronze badges

PCA plot in R coloured by sample type

Awarded Sep 19 at 4:36

Athon

231 silver badge4 bronze badges

How to measure the total size of a fastq file in base pairs?

Awarded Sep 7 at 14:40

Laura

8815 silver badges11 bronze badges

DimPlot - How to highlight cells with identity colors?

Awarded Sep 5 at 17:21

Johnny Rocketfingers

591 silver badge4 bronze badges

Changing the record id in a FASTA file using BioPython

Awarded Sep 4 at 12:07

BioGeek

4965 silver badges15 bronze badges

How to filter a SAM file by a bed file?

Awarded Sep 3 at 19:07

Kyle

1711 silver badge7 bronze badges

Cannot blast database created with blastdb_aliastool: BLAST Database error: No alias or index file found

Awarded Sep 2 at 19:57

MrTomRod

1911 silver badge4 bronze badges

Count of each sequence length from a fasta file with header using len function of python

Awarded Sep 2 at 9:47

Kishor Kumar Sarker

711 silver badge6 bronze badges

#1 Parsing trouble java.lang.NumberFormatException in GSEA 4.2.1

Awarded Sep 1 at 13:48

Hong

211 silver badge3 bronze badges

How to import data from cell ranger to R (Seurat)?

Awarded Aug 28 at 16:45

Mystral

111 silver badge3 bronze badges

How to extract the protein fasta file from a genbank file?

Awarded Aug 28 at 7:56

Cleb

7437 silver badges18 bronze badges

"Sequence Duplication Levels" module still fails after pre-processing Illumina data

Awarded Aug 27 at 7:26

yy97

431 silver badge3 bronze badges

Is there an "official" standard usage of Red and Green on differential gene expression heatmaps?

Awarded Aug 25 at 19:06

Dan

1361 silver badge4 bronze badges

Hosting IGV web on a server

Awarded Aug 23 at 13:18

Migwell

3753 silver badges8 bronze badges

Filtering Sequences (entries) by headers ID from a Fasta file database

Awarded Aug 17 at 13:56

Fabricio

111 silver badge2 bronze badges

Highly variable genes analysis by DESeq2

Awarded Aug 16 at 6:48

Nikita Vlasenko

2,5383 gold badges24 silver badges37 bronze badges

Compressing read data (converting fastq to fastq.gz) on Windows

Awarded Aug 6 at 1:01

Tarannom

111 silver badge2 bronze badges

Running MaxQuant on Linux

Awarded Aug 1 at 13:50

Manuel

1131 silver badge5 bronze badges

Pulling out a certain gene in a volcano plot

Awarded Aug 1 at 7:00

mmpp

3714 silver badges18 bronze badges

Renaming samples in vcf file

Awarded Aug 1 at 2:03

CoDa

451 silver badge6 bronze badges

Convert PAF format to SAM/BAM format

Awarded Jul 31 at 20:04

Paul Endymion

3522 silver badges14 bronze badges

How can I obtain a list of all NCBI gene ID's along with their full name, symbol, and also known as symbols?

Awarded Jul 20 at 8:05

BioBroo

1231 silver badge4 bronze badges

How to split a Seurat cluster in several subclusters?

Awarded Jun 29 at 9:10

Shani

211 silver badge2 bronze badges

postgreSQL error: "ERROR: invalid input syntax for type numeric: NULL" [closed]

Awarded Jun 28 at 1:08

charlieb

111 silver badge2 bronze badges

How I can reproduce this heat map

Awarded Jun 27 at 23:42

Angel

1,98111 silver badges39 bronze badges

how to obtain only one cluster's data (.csv file) in Seurat

Awarded Jun 19 at 19:55

hua

4411 gold badge7 silver badges14 bronze badges

Using `install.packages` with conda-managed R

Awarded Jun 19 at 14:05

Ram RS

2,08610 silver badges28 bronze badges

Reading multiple raw files in Seurat

Awarded Jun 17 at 17:10

mmpp

3714 silver badges18 bronze badges

Help to create a dataframe in Python from a FASTA file

Awarded Jun 13 at 18:18

HelpNeederStudent

2172 silver badges12 bronze badges

BAM to gene expression matrix (UMI counts per gene per cell),10X

Awarded Jun 8 at 3:10

h3ab74

8365 silver badges14 bronze badges

Get residue position from Pymol Selection

Awarded May 25 at 16:49

C. Zeil

1211 silver badge6 bronze badges

How to convert a BAM file into a VCF file

Awarded May 25 at 3:16

Scott XU

1351 silver badge5 bronze badges

Import gene list to Seurat to define cell types

Awarded May 19 at 14:08

SherlockLTS

311 silver badge3 bronze badges

Is it possible to identify cells that are expressing two or more genes in Seurat?

Awarded May 15 at 21:35

Gabriel Alencar

411 silver badge4 bronze badges

How can I remove (non-trivial) duplicates from a VCF file?

Awarded May 10 at 23:56

terdon♦

9,6624 gold badges21 silver badges47 bronze badges

Installing DESeq2 in Ubuntu

Awarded May 9 at 22:21

aerijman

6455 silver badges13 bronze badges

How does MinKNOW classify 1D reads as "pass" or "fail"?

Awarded May 7 at 17:11

Mark Amery

2772 silver badges13 bronze badges

Convert rs ID of one hg build to rs IDs of another build

Awarded Apr 27 at 12:48

Rob John

2212 silver badges6 bronze badges

How do you visualize minimap2's PAF output format?

Awarded Apr 17 at 8:43

0x90

1,4279 silver badges17 bronze badges

How to interpret the GROMACS MD Simulation RMSD Graph?

Awarded Apr 13 at 18:03

Zheng Keong Ng

1992 silver badges9 bronze badges

What is a poly(T) primer anchor sequence?

Awarded Apr 13 at 4:57

gc5

1,78317 silver badges31 bronze badges

Using bioconductor from Python

Awarded Apr 7 at 4:47

An Ignorant Wanderer

5354 silver badges12 bronze badges

How to interpret duplication from MultiQC/FastQC?

Awarded Apr 6 at 11:55

SmallChess

2,7393 gold badges18 silver badges35 bronze badges

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