Bioinformatics Stack Exchange by Kiwix

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

Most popular questions

158 Why does the SARS-Cov2 coronavirus genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa (33 a's)? 2020-01-25T00:55:19.673

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

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

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

26 What is the difference between FASTA, FASTQ, and SAM file formats? 2017-05-16T18:37:27.773

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

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

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

25 Why does the FASTA sequence for coronavirus look like DNA, not RNA? 2020-02-09T17:13:16.303

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

23 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

22 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

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

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

19 What Ensembl genome version should I use for alignments? (e.g. toplevel.fa vs. primary_assembly.fa) 2017-06-07T13:23:52.380

19 Since every human has a different DNA (different combinations of C, G, A, T) what does it mean to have the genome done? 2020-03-24T14:41:29.067

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

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

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

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

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

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

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

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

17 How can we distinguish between true zero and dropout-zero counts in single-cell RNA-seq? 2017-06-13T13:03:09.127

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

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

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

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

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

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

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

16 How can I downsample a BAM file while keeping both reads in pairs? 2017-06-02T23:44:44.637

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

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

15 What's the best way to download data from the SRA? Is it really this slow? 2017-06-03T11:43:30.357

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

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

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

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

14 Merge hundreds of small BAM files into a single BAM file 2017-05-19T05:50:24.497

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

14 How can I extract normalized read count values from DESeq2 results? 2017-05-22T14:51:27.550

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

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

14 Downloading a reference Genome for Bowtie2 2017-05-31T22:56:26.803

14 Why would someone use a CRAM instead of a BAM? 2018-02-26T00:16:32.437

14 Biopython Phylogenetic Tree replace branch tip labels by sequence logos 2018-05-21T12:41:02.080

14 Is it possible for coronavirus or SARS to be synthetic? 2020-02-04T01:54:06.940

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

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