User Konrad Rudolph - Bioinformatics Stack Exchange

61 votes

Accepted

What is the difference between FASTA, FASTQ, and SAM file formats?

answered Jun 2, 2017 at 12:16

32 votes

Accepted

How to compute RPKM in R?

answered May 17, 2017 at 10:46

18 votes

R package development: How does one automatically install Bioconductor packages upon package installation?

answered Jan 23, 2018 at 13:57

15 votes

Are there any RepBase alternatives for genome-wide repeat element annotations?

answered Jun 1, 2017 at 12:15

13 votes

What methods are available to find a cutoff value for non-expressed genes in RNA-seq?

answered Jun 13, 2017 at 11:13

11 votes

Downloading a reference Genome for Bowtie2

answered Jun 1, 2017 at 9:38

10 votes

Accepted

Calculating average coverage for .bam files (sequence data)

answered Jul 4, 2020 at 13:26

9 votes

Accepted

Converting gene names from one public database format to another

answered Jun 6, 2017 at 14:16

9 votes

What are the ways to keep track of branches in the analysis?

answered Jun 15, 2017 at 12:47

7 votes

Fast way to count number of reads and number of bases in a fastq file?

answered Jun 28, 2017 at 15:22

7 votes

How to append numbers only on duplicates sequence names?

answered Jul 4, 2017 at 13:10

7 votes

Accepted

Merging sequencing data for ChIP-seq experiments

answered Jun 3, 2017 at 12:48

7 votes

How do I efficiently subset a very large line-based file?

answered Jun 5, 2017 at 12:49

6 votes

How can I extract normalized read count values from DESeq2 results?

answered May 24, 2017 at 10:17

6 votes

Accepted

Count genomic ranges

answered Jun 13, 2017 at 14:04

6 votes

Why does the FASTA sequence for coronavirus look like DNA, not RNA?

answered Feb 10, 2020 at 16:22

6 votes

Accepted

Is there an efficient way to check an input BAM in R?

answered May 2, 2018 at 8:38

6 votes

Accepted

Off-by-one error when mapping Ensembl IDs to gene symbols

answered May 3, 2018 at 12:31

5 votes

How should the popular press compare similarity of genomes?

answered Apr 4, 2018 at 9:22

5 votes

Error creating indices using STAR

answered May 24, 2018 at 9:32

5 votes

Accepted

Use of heterozygous SNPs in cancer research: why?

answered Jun 6, 2018 at 9:09

5 votes

How can I find mutations associated with disease in human histone residues?

answered Jul 14, 2017 at 16:12

5 votes

What is the fastest way to calculate the number of unknown nucleotides in FASTA / FASTQ files?

answered Jun 1, 2017 at 17:10

5 votes

Generic HMM solvers in bioinformatics?

answered Jun 2, 2017 at 10:59

5 votes

Cannot install chromosomer

answered Aug 9, 2017 at 16:21

4 votes

How to convert fasta file to tab delimited file

answered Oct 17, 2017 at 16:45

4 votes

Estimate the length of poly-A tails from randomly-primed RNAseq data

answered Dec 1, 2017 at 17:27

4 votes

Accepted

How does htslib/samtools access optional BAM fields?

answered Apr 3, 2018 at 10:53

4 votes

Are there any rolling hash functions that can hash a DNA sequence and its reverse complement to the same value?

answered May 17, 2017 at 10:18

4 votes

Multiple sequence alignment with R

answered Aug 3, 2017 at 9:31

Stack Exchange Network

55 Answers

What is the difference between FASTA, FASTQ, and SAM file formats?

How to compute RPKM in R?

R package development: How does one automatically install Bioconductor packages upon package installation?

Are there any RepBase alternatives for genome-wide repeat element annotations?

What methods are available to find a cutoff value for non-expressed genes in RNA-seq?

Downloading a reference Genome for Bowtie2

Calculating average coverage for .bam files (sequence data)

Converting gene names from one public database format to another

What are the ways to keep track of branches in the analysis?

Fast way to count number of reads and number of bases in a fastq file?

How to append numbers only on duplicates sequence names?

Merging sequencing data for ChIP-seq experiments

How do I efficiently subset a very large line-based file?

How can I extract normalized read count values from DESeq2 results?

Count genomic ranges

Why does the FASTA sequence for coronavirus look like DNA, not RNA?

Is there an efficient way to check an input BAM in R?

Off-by-one error when mapping Ensembl IDs to gene symbols

How should the popular press compare similarity of genomes?

Error creating indices using STAR

Use of heterozygous SNPs in cancer research: why?

How can I find mutations associated with disease in human histone residues?

What is the fastest way to calculate the number of unknown nucleotides in FASTA / FASTQ files?

Generic HMM solvers in bioinformatics?

Cannot install chromosomer

How to convert fasta file to tab delimited file

Estimate the length of poly-A tails from randomly-primed RNAseq data

How does htslib/samtools access optional BAM fields?

Are there any rolling hash functions that can hash a DNA sequence and its reverse complement to the same value?

Multiple sequence alignment with R