User winni2k

27 votes

Accepted

What is a quick way to find the reverse complement in bash

answered Apr 15, 2019 at 9:46

11 votes

Random access on a FASTQ file

answered Jun 19, 2017 at 14:06

9 votes

Delete all 4 lines of a fastq read from a fastq file using read ID

answered Nov 9, 2018 at 9:23

8 votes

Accepted

Is spark widely used in bioinformatics?

answered Jun 4, 2017 at 1:33

6 votes

What is the standard way to work with a diploid reference genome? Complementary strands?

answered Jun 26, 2017 at 7:23

5 votes

Random access on a FASTQ file

answered Jun 19, 2017 at 13:15

4 votes

Hardware Requirements (specs) for Bioinformatics-dedicated desktop

answered Feb 4, 2019 at 7:59

4 votes

Is there a command line tool to split a SAM/BAM file by CB (cell barcode) tag?

answered Apr 7, 2020 at 18:44

4 votes

Accepted

Imputing missing genotypes from separate genotyping panels

answered Jun 1, 2017 at 15:22

4 votes

Expected allele frequency distribution of SNVs in real NGS data

answered Jun 4, 2017 at 1:17

4 votes

Are there open-sourced graph-based variant callers?

answered Feb 10, 2021 at 12:32

3 votes

Converting a VCF into a FASTA given a reference with Python, R

answered Apr 16, 2019 at 13:32

3 votes

Accepted

Base abbreviations other than ACTGU in sequence file

answered May 5, 2021 at 16:10

3 votes

Accepted

How to maximize fastq parsing with FastqGeneralIterator (Bio.SeqIO.QualityIO)

answered Jun 23, 2017 at 13:01

3 votes

Filtering imputed GWAS SNPs based on a MAF difference of 10%

answered Jun 4, 2017 at 23:11

3 votes

Accepted

Convert local alignments to spliced alignments in SAM file

answered Nov 18, 2018 at 8:35

2 votes

How to interpret contig-alignment.psa produced by velvet

answered Nov 18, 2018 at 8:39

2 votes

Sampling haplotypes

answered Nov 27, 2018 at 19:28

2 votes

Accepted

Sampling haplotypes

answered Dec 6, 2018 at 17:28

2 votes

Accepted

Is there a tool that can perform a read-group-aware mpileup from a single file?

answered May 5, 2020 at 13:15

2 votes

Produce .vcf file of ALL mutations in .bam file

answered Aug 13, 2020 at 20:06

2 votes

calling diploid SNVs from long reads

answered Nov 26, 2018 at 12:59

2 votes

Accepted

How do I compare measured ratios to calculated ratios in peptide mass spectrometry?

answered Jun 10, 2017 at 15:40

2 votes

Accepted

Selecting sites from VCF which have an alt AD > 10

answered Jul 4, 2017 at 16:24

2 votes

Recommendations for missing value imputation - DNA methylation data

answered Sep 18, 2017 at 10:24

2 votes

How to filter info score post-imputation?

answered Feb 16, 2018 at 21:43

2 votes

Impute phenotype under some constraints

answered Mar 10, 2018 at 17:38

2 votes

What is the fastest way to get the reverse complement of a DNA sequence in python?

answered Apr 6, 2018 at 20:37

2 votes

Imputation of dog genotype

answered May 9, 2021 at 12:06

2 votes

Error in running Mutect2

answered Jan 31, 2022 at 13:57

Stack Exchange Network

46 Answers

What is a quick way to find the reverse complement in bash

Random access on a FASTQ file

Delete all 4 lines of a fastq read from a fastq file using read ID

Is spark widely used in bioinformatics?

What is the standard way to work with a diploid reference genome? Complementary strands?

Random access on a FASTQ file

Hardware Requirements (specs) for Bioinformatics-dedicated desktop

Is there a command line tool to split a SAM/BAM file by CB (cell barcode) tag?

Imputing missing genotypes from separate genotyping panels

Expected allele frequency distribution of SNVs in real NGS data

Are there open-sourced graph-based variant callers?

Converting a VCF into a FASTA given a reference with Python, R

Base abbreviations other than ACTGU in sequence file

How to maximize fastq parsing with FastqGeneralIterator (Bio.SeqIO.QualityIO)

Filtering imputed GWAS SNPs based on a MAF difference of 10%

Convert local alignments to spliced alignments in SAM file

How to interpret contig-alignment.psa produced by velvet

Sampling haplotypes

Sampling haplotypes

Is there a tool that can perform a read-group-aware mpileup from a single file?

Produce .vcf file of ALL mutations in .bam file

calling diploid SNVs from long reads

How do I compare measured ratios to calculated ratios in peptide mass spectrometry?

Selecting sites from VCF which have an alt AD > 10

Recommendations for missing value imputation - DNA methylation data

How to filter info score post-imputation?

Impute phenotype under some constraints

What is the fastest way to get the reverse complement of a DNA sequence in python?

Imputation of dog genotype

Error in running Mutect2