User ABCD

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

10k 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

654 views

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

asked Jan 23, 2019 at 4:56

7 votes

2 answers

2k views

Is this a low complexity region in our human genome?

asked Jan 9, 2018 at 6:36

7 votes

1 answer

693 views

How to simulate "base error rate" in art_illumina?

asked Jul 5, 2017 at 6:55

6 votes

1 answer

702 views

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

asked Sep 4, 2017 at 7:54

6 votes

1 answer

491 views

How to filter out cross alignments from a BED file?

asked May 19, 2017 at 5:49

6 votes

3 answers

1k views

Somatic tumor only variant calling?

asked Oct 31, 2017 at 23:30

5 votes

1 answer

985 views

How to show only my read on IGV?

asked Jan 5, 2018 at 3:11

5 votes

3 answers

742 views

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

asked Oct 12, 2017 at 23:24

5 votes

1 answer

848 views

Simplest way to work out structural variant type?

asked Jul 16, 2018 at 12:57

5 votes

1 answer

975 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

193 views

What is "block-compressed" file in samtools?

asked Nov 13, 2018 at 10:04

4 votes

1 answer

125 views

Simulate and test CNV workflow?

asked Nov 24, 2018 at 17:40

4 votes

1 answer

253 views

How should I address batch effects in my experiment?

asked Nov 28, 2018 at 9:16

3 votes

1 answer

754 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

417 views

Protein expression units?

asked Apr 26, 2018 at 4:49

2 votes

2 answers

559 views

How to filter for "CAF=0.5747,0.4253"

asked Jun 1, 2018 at 6:49

1 vote

1 answer

93 views

What does "ALT+ cancer cells", the plus sign mean?

asked Sep 18, 2018 at 0:12

1 vote

1 answer

356 views

Using Broad Institute RNAseq pipeline

asked Sep 21, 2018 at 2:30

1 vote

1 answer

3k views

How to interpret duplication from MultiQC/FastQC?

asked Oct 25, 2018 at 2:11

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?

Is this a low complexity region in our human genome?

How to simulate "base error rate" in art_illumina?

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

How to filter out cross alignments from a BED file?

Somatic tumor only variant calling?

How to show only my read on IGV?

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

Simplest way to work out structural variant type?

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"

What does "ALT+ cancer cells", the plus sign mean?

Using Broad Institute RNAseq pipeline

How to interpret duplication from MultiQC/FastQC?