Bioinformatics Stack Exchange by Kiwix

Q&A for researchers, developers, students, teachers, and end users interested in bioinformatics

Most popular questions

36 What's the most efficient file format for the storage of DNA sequences? 2017-05-16T18:01:06.383

31 Feature annotation: RefSeq vs Ensembl vs Gencode, what's the difference? 2017-05-16T19:24:16.303

21 Read length distribution from FASTA file 2017-05-17T04:38:52.420

21 Why sequence the human genome at 30x coverage? 2017-08-04T15:10:40.400

20 Are there any rolling hash functions that can hash a DNA sequence and its reverse complement to the same value? 2017-05-16T19:15:57.957

19 How to version the code and the data during the analysis? 2017-05-18T09:27:51.110

19 Why do some assemblers require an odd-length kmer for the construction of De Brujin graphs? 2017-05-19T18:34:20.767

18 What happens if a major bug is discovered in a bioinformatic package that has been used in published literature? 2017-11-14T00:26:35.937

16 Accuracy of the original human DNA datasets sequenced by Human Genome Project? 2017-05-16T18:14:20.903

16 Uppercase vs lowercase letters in reference genome 2017-05-24T03:26:50.163

14 How can I call structural variants (SVs) from pair-end short read resequencing data? 2017-05-18T14:28:47.653

14 Tools for simulating Oxford Nanopore reads 2017-05-22T18:19:53.483

13 Convert a BAM file from one reference to another? 2017-05-16T20:00:43.050

13 Single-sample vs. joint genotyping 2017-05-17T13:02:17.453

13 How to simulate NGS reads, controlling sequence coverage? 2017-05-17T16:26:16.783

13 How to convert FASTA to BED 2017-05-18T00:14:58.347

13 Confirm success or failure RNA-Seq normalization 2017-05-18T00:28:24.290

13 How can I improve a long-read assembly with a repetitive genome? 2017-05-25T11:46:36.237

13 What is the fastest way to calculate the number of unknown nucleotides in FASTA / FASTQ files? 2017-06-01T16:47:02.727

13 How exactly is "effective length" used in FPKM calculated? 2017-06-01T19:49:22.177

13 What is the actual cause of excessive zeroes in single cell RNA-seq data? Is it PCR? 2017-10-20T08:50:43.333

12 Mapping drug names to ATC codes 2017-05-16T18:28:49.047

12 Compare alignment quality of multiple sequencing runs aligned against the same reference genome 2017-05-17T02:18:01.720

12 How to compute RPKM in R? 2017-05-17T10:28:32.203

12 How to make a distinction between the "classical" de Bruijn graph and the one described in NGS papers? 2017-05-19T10:32:45.047

12 How to deal with heterozygosity during polishing of genome assembly based on long reads? 2017-05-21T11:49:58.693

12 Publicly available genome sequence database for viruses? 2017-06-07T16:54:42.373

12 Why Bioconductor? 2017-06-11T01:28:57.607

11 What are the optimal parameters for docking a large ligand using Hex? 2017-05-16T18:31:28.570

11 Alignment based vs reference-free (transcriptome analysis)? 2017-05-17T05:19:48.690

11 Normalization methods with RNA-Seq ERCC spike in? 2017-05-17T05:24:25.273

11 The state, limitations and comparisons of large variant stores 2017-05-22T16:14:17.213

11 Designing a lab NGS file database schema 2017-05-22T16:32:40.663

11 Is it possible to perform MinION sequencing offline? 2017-05-31T06:22:09.180

11 Why is bwa-mem the standard algorithm when using bwa? 2017-06-03T13:58:26.980

11 How do I efficiently subset a very large line-based file? 2017-06-05T12:49:24.763

11 BAM to BigWig without intermediary BedGraph 2017-06-07T07:20:47.170

11 Random access on a FASTQ file 2017-06-19T13:15:22.910

11 Is there a standard k-mer count file format? 2017-07-26T01:44:09.730

11 What is the fastest way to get the reverse complement of a DNA sequence in python? 2018-02-20T05:10:43.110

10 Improve a reference genome with sequencing data 2017-05-18T03:11:37.330

10 Understanding DESeq2 design, contrast and results 2017-05-19T14:40:13.787

10 Given a VCF of a human genome, how do I assess the quality against known SNVs? 2017-05-20T21:49:51.210

10 What are the advantages and disadvantages between using KEGG or Reactome? 2017-05-24T07:35:31.097

10 Is there an easy way to create a summary of a VCF file (v4.1) with structural variations? 2017-05-28T21:40:13.940

10 How does the BWA-MEM algorithm assign its mapping qualities? 2017-05-30T21:36:46.213

10 Are there any RepBase alternatives for genome-wide repeat element annotations? 2017-06-01T11:11:09.893

10 Generic HMM solvers in bioinformatics? 2017-06-02T07:13:13.107

10 Are there any databases of templates for common bioinformatic file formats? 2017-06-02T14:08:49.563

10 What is the best method to estimate a phylogenetic tree from a large dataset of >1000 loci and >100 species 2017-06-10T03:57:26.523


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