User ShanZhengYang

1

12

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3

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340

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

Jan 15 '19 at 14:30 Daniel Standage 4,553

3

12

votes

2

answers

3k

views

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

r bioconductor

Jan 23 '18 at 13:57 Konrad Rudolph 4,605

2

11

votes

3

answers

5k

views

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

r python fasta vcf samtools

Jul 3 at 15:12 winni2k 1,941

1

8

votes

2

answers

4k

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

vcf variant-calling maf

May 27 '20 at 8:34 Amarinder Singh Thind 11

8

votes

4

answers

1k

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 1,302

7

votes

2

answers

2k

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Extracting the CIGAR string from a BAM via Python?

python bam pysam cigar

Mar 4 at 15:05 The Unfun Cat 421

7

votes

2

answers

113

views

How to release an R package with several bed files?

r bed

Jan 10 '19 at 8:24 llrs 4,532

1

7

votes

3

answers

3k

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

bam samtools reads

Oct 2 '17 at 19:22 Bioathlete 2,526

7

votes

3

answers

600

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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 694

7

votes

5

answers

471

views

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

motifs software-recommendation

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

6

votes

2

answers

372

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 4,553

6

votes

3

answers

509

views

Generating the reconstructed alignment from BAM

r python bam alignment sequence-alignment

Nov 26 '18 at 1:59 Colin D 156

6

votes

5

answers

768

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 1,786

6

votes

2

answers

237

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 4,605

1

5

votes

3

answers

7k

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How to concatenate "by chromosome"-VCFs?

vcf vcftools

Jan 15 '18 at 18:30 Pierre 1,438

5

votes

2

answers

548

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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 2,745

1

4

votes

1

answer

2k

views

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

python vcf

Dec 15 '17 at 19:43 Bioathlete 2,526

4

votes

2

answers

546

views

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

repeat centromere telomere

Oct 4 '17 at 1:27 user172818 5,441

1

4

votes

1

answer

265

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 1,396

4

votes

2

answers

211

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 7,597

1

3

votes

2

answers

350

views

Parse BAM by insertion size and get genomic coordinates

bam samtools

Feb 9 '18 at 14:13 Pierre 1,438

2

votes

1

answer

725

views

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

bam public-databases maf

Jan 26 '18 at 19:09 gringer♦ 10.6k

0

votes

2

answers

534

views

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

bigwig validation

Feb 3 '18 at 16:59 Alex Reynolds 2,745

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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

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

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

Extracting the CIGAR string from a BAM via Python?

How to release an R package with several bed files?

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

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?

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

Generating the reconstructed alignment from BAM

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

How to concatenate "by chromosome"-VCFs?

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?

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

Parse BAM by insertion size and get genomic coordinates

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

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