User SmallChess

19 votes

7 answers

15k views

How to convert FASTA to BED

asked May 18, 2017 at 0:14

16 votes

2 answers

2k views

Alignment based vs reference-free (transcriptome analysis)?

asked May 17, 2017 at 5:19

15 votes

10 answers

3k views

How to simulate NGS reads, controlling sequence coverage?

asked May 17, 2017 at 16:26

14 votes

2 answers

4k views

Normalization methods with RNA-Seq ERCC spike in?

asked May 17, 2017 at 5:24

13 votes

2 answers

2k views

How to read structural variant VCF?

asked May 29, 2017 at 6:25

9 votes

2 answers

11k views

How to use Python to count k-mers?

asked Jun 8, 2017 at 4:54

9 votes

2 answers

9k views

Why Ti/Tv ratio?

asked May 25, 2018 at 12:55

8 votes

4 answers

11k views

What reasons are there to choose Illumina if PacBio provides longer and better reads?

asked Jan 31, 2019 at 5:39

7 votes

2 answers

682 views

How to check if indels in VCF files are left or right aligned?

asked Jan 23, 2019 at 4:56

7 votes

1 answer

732 views

How to simulate "base error rate" in art_illumina?

asked Jul 5, 2017 at 6:55

7 votes

2 answers

2k views

Is this a low complexity region in our human genome?

asked Jan 9, 2018 at 6:36

6 votes

1 answer

711 views

How to build a BAM header file with htslib in C++?

asked Sep 4, 2017 at 7:54

6 votes

3 answers

1k views

Somatic tumor only variant calling?

asked Oct 31, 2017 at 23:30

6 votes

1 answer

493 views

How to filter out cross alignments from a BED file?

asked May 19, 2017 at 5:49

5 votes

1 answer

1k views

How to show only my read on IGV?

asked Jan 5, 2018 at 3:11

5 votes

1 answer

858 views

Simplest way to work out structural variant type?

asked Jul 16, 2018 at 12:57

5 votes

3 answers

761 views

Read sorted and indexed BAM files faster in C++?

asked Oct 12, 2017 at 23:24

5 votes

1 answer

1k views

Why do I get so many insertions from Minimap2 on my Nanopore WGS?

asked Feb 8, 2019 at 6:11

4 votes

1 answer

92 views

Does UCSC definition for telomere making sense?

asked Mar 11, 2019 at 6:09

4 votes

3 answers

2k views

What do the FASTQ file names mean here?

asked Jun 29, 2019 at 14:21

4 votes

1 answer

214 views

What is "block-compressed" file in samtools?

asked Nov 13, 2018 at 10:04

4 votes

1 answer

127 views

Simulate and test CNV workflow?

asked Nov 24, 2018 at 17:40

4 votes

1 answer

256 views

How should I address batch effects in my experiment?

asked Nov 28, 2018 at 9:16

3 votes

1 answer

769 views

How to use C++ htslib to read VCF contig name and size?

asked Feb 28, 2018 at 9:57

2 votes

1 answer

124 views

What's "signal" in gene expression?

asked Apr 16, 2018 at 7:57

2 votes

2 answers

438 views

Protein expression units?

asked Apr 26, 2018 at 4:49

2 votes

2 answers

571 views

How to filter for "CAF=0.5747,0.4253"

asked Jun 1, 2018 at 6:49

1 vote

0 answers

89 views

Train a new basecalling model for nanopore?

asked Mar 6, 2020 at 15:39

1 vote

3 answers

419 views

How to filter allele frequency VEP with bcftools?

asked Nov 4, 2020 at 17:28

Stack Exchange Network

35 Questions

How to convert FASTA to BED

Alignment based vs reference-free (transcriptome analysis)?

How to simulate NGS reads, controlling sequence coverage?

Normalization methods with RNA-Seq ERCC spike in?

How to read structural variant VCF?

How to use Python to count k-mers?

Why Ti/Tv ratio?

What reasons are there to choose Illumina if PacBio provides longer and better reads?

How to check if indels in VCF files are left or right aligned?

How to simulate "base error rate" in art_illumina?

Is this a low complexity region in our human genome?

How to build a BAM header file with htslib in C++?

Somatic tumor only variant calling?

How to filter out cross alignments from a BED file?

How to show only my read on IGV?

Simplest way to work out structural variant type?

Read sorted and indexed BAM files faster in C++?

Why do I get so many insertions from Minimap2 on my Nanopore WGS?

Does UCSC definition for telomere making sense?

What do the FASTQ file names mean here?

What is "block-compressed" file in samtools?

Simulate and test CNV workflow?

How should I address batch effects in my experiment?

How to use C++ htslib to read VCF contig name and size?

What's "signal" in gene expression?

Protein expression units?

How to filter for "CAF=0.5747,0.4253"

Train a new basecalling model for nanopore?

Recommended workflow for RNA long read Kallisto-like TPM estimation?

How to filter allele frequency VEP with bcftools?