User 719016

27 votes

4 answers

6k views

Why sequence the human genome at 30x coverage?

asked Aug 4, 2017 at 15:10

9 votes

2 answers

6k views

samtools depth print out all positions

asked Jun 7, 2017 at 8:39

8 votes

3 answers

1k views

Least present k-mers in the human genome

asked Nov 15, 2017 at 10:22

8 votes

2 answers

450 views

Convert bam file to highly compressible bam

asked Mar 12, 2018 at 6:02

7 votes

6 answers

2k views

bed file with N regions of GRCh38 reference?

asked Feb 13, 2018 at 9:45

7 votes

1 answer

783 views

low-memory high-speed replacement for Picard MarkDuplicates

asked Dec 11, 2017 at 15:45

7 votes

1 answer

785 views

ethnicity check either from bam or vcf files

asked Jan 9, 2018 at 9:41

7 votes

3 answers

458 views

GRCh38 vcf file with common cancer mutations

asked Jun 15, 2017 at 11:56

7 votes

1 answer

456 views

samtools mpileup empty when filtering out flags

asked May 24, 2017 at 15:37

7 votes

2 answers

310 views

variant calling on ChIP-seq style data: samtools mpileup with minimal filters

asked May 26, 2017 at 13:23

7 votes

1 answer

272 views

Server for finding kmers in set of sequences

asked Sep 7, 2017 at 13:46

6 votes

1 answer

161 views

checks for spike-in sequence controls

asked Aug 31, 2017 at 7:41

6 votes

2 answers

79 views

Does the MAPQ=0 fraction of a BAM file depend on the insert sizes?

asked Jan 9, 2018 at 9:56

5 votes

2 answers

814 views

Interpreting 0x200 flag in bwa-mem alignments

asked Dec 4, 2017 at 14:43

5 votes

2 answers

341 views

GRCh38 centromeres mappability

asked Aug 14, 2017 at 8:33

5 votes

2 answers

133 views

Creating a new reference genome B by changing genome A with mismatches from BAM file without long reads

asked Oct 24, 2017 at 8:14

5 votes

4 answers

345 views

tool to visualize a collection of phylogenetic trees

asked Nov 1, 2019 at 10:35

4 votes

1 answer

70 views

alternatives to MEDIPS to analyse MeDIP datasets

asked Jul 10, 2017 at 9:40

4 votes

2 answers

3k views

how is the DNA Integrity Number (DIN) calculated in Bioanalyzer/TapeStation?

asked Jul 12, 2017 at 9:36

4 votes

3 answers

536 views

what percentage of the human genome is MAPQ=0?

asked Jul 17, 2017 at 12:22

3 votes

1 answer

143 views

IGV faster loading remote bigWig files

asked Aug 10, 2017 at 12:24

3 votes

3 answers

358 views

IGV jump to rsID location

asked Oct 25, 2017 at 13:22

3 votes

1 answer

312 views

Database of copy number alterations in different cancer types

asked Aug 30, 2017 at 8:53

3 votes

1 answer

239 views

genes with highest RPKM/FPKM for a human RNA-seq experiment?

asked Sep 5, 2017 at 10:53

3 votes

2 answers

275 views

Selecting 65000 SNPs where AF is close to 0.5 in all or most populations

asked Feb 8, 2019 at 14:10

3 votes

1 answer

75 views

predict the foldability of single-stranded DNA molecules

asked Jan 17, 2018 at 10:16

3 votes

1 answer

446 views

calculating phylogenetic tree from pairwise distances

asked Aug 9, 2021 at 17:31

2 votes

1 answer

92 views

De novo antibody sequencing fromMS/MS Ion Trap proteomics raw signal

asked Apr 4, 2022 at 10:13

2 votes

1 answer

320 views

how to download all metadata for a single TCGA dataset and link to data file UUIDs?

asked Jan 4 at 13:09

2 votes

1 answer

68 views

where to find pathogenicity metadata for E.coli genomes

asked Oct 9, 2019 at 9:48

Stack Exchange Network

54 Questions

Why sequence the human genome at 30x coverage?

samtools depth print out all positions

Least present k-mers in the human genome

Convert bam file to highly compressible bam

bed file with N regions of GRCh38 reference?

low-memory high-speed replacement for Picard MarkDuplicates

ethnicity check either from bam or vcf files

GRCh38 vcf file with common cancer mutations

samtools mpileup empty when filtering out flags

variant calling on ChIP-seq style data: samtools mpileup with minimal filters

Server for finding kmers in set of sequences

checks for spike-in sequence controls

Does the MAPQ=0 fraction of a BAM file depend on the insert sizes?

Interpreting 0x200 flag in bwa-mem alignments

GRCh38 centromeres mappability

Creating a new reference genome B by changing genome A with mismatches from BAM file without long reads

tool to visualize a collection of phylogenetic trees

alternatives to MEDIPS to analyse MeDIP datasets

how is the DNA Integrity Number (DIN) calculated in Bioanalyzer/TapeStation?

what percentage of the human genome is MAPQ=0?

IGV faster loading remote bigWig files

IGV jump to rsID location

Database of copy number alterations in different cancer types

genes with highest RPKM/FPKM for a human RNA-seq experiment?

Selecting 65000 SNPs where AF is close to 0.5 in all or most populations

predict the foldability of single-stranded DNA molecules

calculating phylogenetic tree from pairwise distances

De novo antibody sequencing fromMS/MS Ion Trap proteomics raw signal

how to download all metadata for a single TCGA dataset and link to data file UUIDs?

where to find pathogenicity metadata for E.coli genomes