User ShanZhengYang

1

12

votes

3

answers

297

views

Given a VCF of a human genome, how do I assess the quality against known SNVs?

Jan 15 '19 at 14:30 Daniel Standage 4,165

3

11

votes

2

answers

2k

views

R package development: How does one automatically install Bioconductor packages upon package installation?

r bioconductor

Jan 23 '18 at 13:57 Konrad Rudolph 4,065

1

10

votes

3

answers

4k

views

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

r python fasta vcf samtools

Apr 16 '19 at 13:32 winni2k 1,465

8

votes

4

answers

851

views

How to manipulate a reference FASTA or bam to include variants from a VCF?

bam fasta vcf reference-genome variation

Jan 15 '19 at 20:10 finswimmer 1,237

7

votes

2

answers

102

views

How to release an R package with several bed files?

r bed

Jan 10 '19 at 8:24 llrs 4,236

7

votes

1

answer

1k

views

Extracting the CIGAR string from a BAM via Python?

python bam pysam cigar

Mar 9 '18 at 19:20 Devon Ryan♦ 16.5k

7

votes

3

answers

489

views

Is there a way to retrieve several SAM fields faster than `samtools view | cut -f`?

bam samtools sam

Aug 25 '17 at 14:27 mattm 664

7

votes

5

answers

386

views

What motif finding software is available for multiple sequences ~10Kb?

motifs software-recommendation

Jun 13 '17 at 22:20 Charles E. Grant 131

1

6

votes

2

answers

2k

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Tools to do VCF to MAF and MAF to VCF conversion?

vcf variant-calling maf

Mar 19 '19 at 10:11 mox 133

6

votes

2

answers

312

views

What is the distribution of indel sizes in a healthy human genome? of insertion:deletion ratios?

variation indel literature-search

Jan 15 '19 at 14:28 Daniel Standage 4,165

6

votes

5

answers

677

views

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

human-genome genome reference-genome

Jan 25 '18 at 12:41 heathobrien 1,726

6

votes

2

answers

199

views

Estimate the length of poly-A tails from randomly-primed RNAseq data

rna-seq software-recommendation rna algorithms

Dec 1 '17 at 17:27 Konrad Rudolph 4,065

5

votes

3

answers

322

views

Generating the reconstructed alignment from BAM

r python bam alignment sequence-alignment

Nov 26 '18 at 1:59 Colin D 141

1

5

votes

3

answers

2k

views

How to check whether all BAM read contain defined read groups?

bam samtools reads

Oct 2 '17 at 19:22 Bioathlete 2,336

5

votes

2

answers

400

views

Is it possible to do alignment within Python? Check variants against reference?

python alignment biopython reference-genome

Sep 19 '17 at 20:31 Alex Reynolds 2,307

1

4

votes

1

answer

1k

views

Using Python, how to convert a pandas DataFrame into a VCF?

python vcf

Dec 15 '17 at 19:43 Bioathlete 2,336

4

votes

2

answers

366

views

How are centromeric/telomeric regions categorized in RepeatMasker? “Other” category?

repeat centromere telomere

Oct 4 '17 at 1:27 user172818♦ 5,096

1

4

votes

1

answer

213

views

Given a Genomic Ranges of SNPs, how to inject these SNPs in genome via BSGenome?

r bioconductor reference-genome snp biostrings

Aug 11 '17 at 13:12 story 1,286

1

3

votes

2

answers

229

views

Parse BAM by insertion size and get genomic coordinates

bam samtools

Feb 9 '18 at 14:13 Pierre 1,403

3

votes

2

answers

179

views

After artificially creating events in a FASTA file, how do I keep track of the old coordinates?

biopython bed structural-variation indel simulated-data

Jul 5 '17 at 8:32 terdon 6,810

2

votes

1

answer

599

views

Downloading an open-source MAF with tumor and normal BAMs?

bam public-databases maf

Jan 26 '18 at 19:09 gringer 9,020

1

2

votes

3

answers

4k

views

How to concatenate “by chromosome”-VCFs?

vcf vcftools

Jan 15 '18 at 18:30 Pierre 1,403

0

votes

2

answers

331

views

Is there a standard method to validate whether a bigWig file is correct?

bigwig validation

Feb 3 '18 at 16:59 Alex Reynolds 2,307

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23 Questions

Given a VCF of a human genome, how do I assess the quality against known SNVs?

R package development: How does one automatically install Bioconductor packages upon package installation?

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

How to manipulate a reference FASTA or bam to include variants from a VCF?

How to release an R package with several bed files?

Extracting the CIGAR string from a BAM via Python?

Is there a way to retrieve several SAM fields faster than `samtools view | cut -f`?

What motif finding software is available for multiple sequences ~10Kb?

Tools to do VCF to MAF and MAF to VCF conversion?

What is the distribution of indel sizes in a healthy human genome? of insertion:deletion ratios?

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

Estimate the length of poly-A tails from randomly-primed RNAseq data

Generating the reconstructed alignment from BAM

How to check whether all BAM read contain defined read groups?

Is it possible to do alignment within Python? Check variants against reference?

Using Python, how to convert a pandas DataFrame into a VCF?

How are centromeric/telomeric regions categorized in RepeatMasker? “Other” category?

Given a Genomic Ranges of SNPs, how to inject these SNPs in genome via BSGenome?

Parse BAM by insertion size and get genomic coordinates

After artificially creating events in a FASTA file, how do I keep track of the old coordinates?

Downloading an open-source MAF with tumor and normal BAMs?

How to concatenate “by chromosome”-VCFs?

Is there a standard method to validate whether a bigWig file is correct?