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Bioinformatics

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Awarded 161 times.
What are all the reference files produced by bwa index, and are these dependent upon whether the reference is zipped?
Awarded Aug 14 at 13:03
How to quickly determine mutations in a read of a sam file?
Awarded Jul 8 at 4:57
How to import a large amount of .bed, .gff, .vcf, .paf, .sam files into an SQL database?
Awarded Jun 29 at 3:03
Run cuffcompare in strand-agnostic mode
Awarded Jun 27 at 4:51
How to calculate overlapping genes between two genome annotation versions
Awarded Apr 11 at 11:49
How to extract fasta from a blastdb
Awarded Mar 20 at 12:35
How do you generate read-length vs read-quality plot for long-read sequencing data (e.g., MinION)?
Awarded Jan 26 at 15:45
How can we find the distance between all residues in a PDB file?
Awarded Sep 21, 2023 at 17:55
How can I extract only insertions from a VCF file?
Awarded Sep 6, 2023 at 5:07
BLAST(n): No hits found
Awarded Sep 6, 2023 at 3:56
Selecting sites from VCF which have an alt AD > 10
Awarded Sep 4, 2023 at 8:17
How to calculate the memory usage of storing kmers in RAM
Awarded Jun 7, 2023 at 3:50
Good / recommended way to archive fastq and bam files?
Awarded Apr 13, 2023 at 8:33
Intersection of two genomic ranges to keep metadata
Awarded Feb 14, 2023 at 17:27
What are the pros and cons of the different basecallers in Oxford Nanopore Technology Sequencing?
Awarded Dec 1, 2022 at 5:50
How to download FASTA sequences from NCBI using the terminal?
Awarded Nov 15, 2022 at 1:10
How to resolve in snakemake error : "Target rules may not contain wildcards."
Awarded Oct 20, 2022 at 12:02
What is a quick way to find the reverse complement in bash
Awarded Aug 31, 2022 at 20:50
Building STAR Genome Index for nanopore RNA sequencing
Awarded Aug 15, 2022 at 15:16
Extract sequence context of high-degree nodes in assembly graphs
Awarded Jul 1, 2022 at 15:04
Pooling data in metagenome assembly
Awarded Jul 1, 2022 at 15:04
Annotation format design
Awarded Jun 6, 2022 at 7:16
Behavior of `--reference` flag with samtools sort
Awarded Jun 6, 2022 at 7:16
What is the index fastq file (sample_I*.fastq.gz) generated when demultiplexing Illumina paired-end runs?
Awarded May 19, 2022 at 8:32
How to apply upperquartile normalization on RSEM expected counts?
Awarded Feb 8, 2022 at 14:41
Is there a database of disease prevalence?
Awarded Dec 8, 2021 at 11:51
How to subset samples from a VCF file?
Awarded Aug 2, 2021 at 10:42
Converting VCF file to PLINK bed/bim/fam files
Awarded Jul 29, 2021 at 20:05
Changing the record id in a FASTA file using BioPython
Awarded Feb 24, 2021 at 22:06
Chimera Alignments
Awarded Jan 19, 2021 at 0:42
Why does this human bam file only have one copy of each chromosome?
Awarded Jan 16, 2021 at 18:17
Tools to create annotated table of variants from VCF
Awarded Jan 13, 2021 at 16:16
Visualisation of long read RNA-Seq splicing
Awarded Jan 5, 2021 at 20:35
A new paper suggests the Corona Virus has "Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1" - What does this mean?
Awarded Oct 26, 2020 at 17:48
Which sequence alignment tools support codon alignment?
Awarded Oct 16, 2020 at 12:20
scRNA-seq multi-dataset integration for small datasets
Awarded Sep 22, 2020 at 4:55
What is the most compact data structure for canonical k-mers with the fastest lookup time?
Awarded Sep 18, 2020 at 0:03
Better aligner than bowtie2?
Awarded Aug 20, 2020 at 15:06
Difference between CPM and TPM and which one for downstream analysis?
Awarded Aug 7, 2020 at 7:26
How to convert fasta file to tab delimited file
Awarded Jun 18, 2020 at 11:24
How do I generate a color-coded tanglegram?
Awarded Jun 8, 2020 at 2:57
Is it possible for coronavirus or SARS to be synthetic?
Awarded Mar 29, 2020 at 7:20
Since every human has a different DNA (different combinations of C, G, A, T) what does it mean to have the genome done? [closed]
Awarded Mar 25, 2020 at 21:25
Which quality score encoding does PacBio use?
Awarded Feb 17, 2020 at 20:10
Why does the FASTA sequence for coronavirus look like DNA, not RNA?
Awarded Feb 10, 2020 at 20:00
Can open-source software be peer-reviewed and published?
Awarded Feb 6, 2020 at 18:30
Why does the SARS-Cov2 coronavirus genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa (33 a's)?
Awarded Jan 25, 2020 at 16:30
Why does a very strong BLAST hit get lost when I change num_alignments, num_descriptions or max_target_seqs parameter?
Awarded Dec 11, 2019 at 16:40
How can I calculate gene_length for RPKM calculation from counts data?
Awarded Nov 7, 2019 at 16:10
How can I systematically detect unknown barcode/adapter sequences within a set of samples?
Awarded Aug 29, 2019 at 8:00
What is the difference between samtools, bamtools, picard, sambamba and biobambam?
Awarded Jul 26, 2019 at 12:10
Converting a VCF into a FASTA given a reference with Python, R
Awarded Jul 18, 2019 at 1:10
When to account for the blacklisted genomic regions in ChIP-seq data analyses?
Awarded Jul 3, 2019 at 20:30
Difference between BWA-backtrack and BWA-MEM
Awarded Jul 1, 2019 at 14:30
What is the difference between a Bioinformatics pipeline and workflow?
Awarded Apr 25, 2019 at 3:15
Library for computing BWT-based alignments
Awarded Mar 21, 2019 at 14:30
State of the art mutation simulation software
Awarded Mar 5, 2019 at 1:05
R package development: How does one automatically install Bioconductor packages upon package installation?
Awarded Feb 26, 2019 at 3:10
Meaning of BWA-MEM MAPQ scores
Awarded Feb 23, 2019 at 20:05
How do I find identical sequences in a FASTA file?
Awarded Jan 30, 2019 at 17:40
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