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Comment: Comment: Alternatives to UCSC genome browser for obtaining gene coordinates
5 months ago by shpak.max ▴ 60
8
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5
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1.1k
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Alternatives to UCSC genome browser for obtaining gene coordinates
browser ucsc
5 months ago by shpak.max ▴ 60
0
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0
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1.1k
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Comment: Comment: Alternatives to UCSC genome browser for obtaining gene coordinates
5 months ago by shpak.max ▴ 60
0
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1
reply
1.1k
views
Comment: Comment: Identify and count gaps in sam/bam files
15 months ago by shpak.max ▴ 60
0
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4
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1.1k
views
Identify and count gaps in sam/bam files
samtools
updated 14 months ago by ★ 1.7k • written 15 months ago by ▴ 60
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0
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725
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Comment: Comment: Correcting a lack of gaps in bwa aln mapping of unpaired reads
15 months ago by shpak.max ▴ 60
0
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2
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725
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Correcting a lack of gaps in bwa aln mapping of unpaired reads
bwa
15 months ago by shpak.max ▴ 60
0
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1
reply
783
views
Comment: Comment: Mismatch between number of reads in fastq and mapped reads
16 months ago by shpak.max ▴ 60
1
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3
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783
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Mismatch between number of reads in fastq and mapped reads
samtools bam
updated 16 months ago by ▴ 600 • written 16 months ago by ▴ 60
0
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0
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996
views
Comment: Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
16 months ago by shpak.max ▴ 60
0
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1
reply
996
views
Comment: Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
16 months ago by shpak.max ▴ 60
0
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4
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996
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Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
GATK UnifiedGenotyper
16 months ago by shpak.max ▴ 60
0
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0
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921
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Comment: Comment: Genotyping sites with N in reference genome
16 months ago by shpak.max ▴ 60
0
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0
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921
views
Comment: Comment: Genotyping sites with N in reference genome
16 months ago by shpak.max ▴ 60
1
vote
4
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921
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Genotyping sites with N in reference genome
GATK UnifiedGenotyper
16 months ago by shpak.max ▴ 60
0
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1
reply
1.2k
views
Comment: Comment: Best way to deal with overlapping read names in merged BAM files
17 months ago by shpak.max ▴ 60
0
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1
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1.2k
views
Comment: Comment: Best way to deal with overlapping read names in merged BAM files
17 months ago by shpak.max ▴ 60
1
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5
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1.2k
views
Best way to deal with overlapping read names in merged BAM files
picard MarkDuplicates
17 months ago by shpak.max ▴ 60
0
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1
reply
1.0k
views
Comment: Comment: Multiple iterations of sorted bam output files with picard SortSam
18 months ago by shpak.max ▴ 60
0
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3
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1.0k
views
Multiple iterations of sorted bam output files with picard SortSam
picard
updated 18 months ago by 154k • written 18 months ago by ▴ 60
0
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0
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1.6k
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Comment: Comment: java version compatible with GATK 3.2.2
18 months ago by shpak.max ▴ 60
0
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1
reply
1.6k
views
Comment: Comment: java version compatible with GATK 3.2.2
18 months ago by shpak.max ▴ 60
0
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0
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1.6k
views
Comment: Comment: java version compatible with GATK 3.2.2
18 months ago by shpak.max ▴ 60
0
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0
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1.6k
views
Comment: Comment: java version compatible with GATK 3.2.2
18 months ago by shpak.max ▴ 60
1
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7
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1.6k
views
java version compatible with GATK 3.2.2
GATK
18 months ago by shpak.max ▴ 60
0
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1
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795
views
Comment: Comment: Merging bam files from different runs
18 months ago by shpak.max ▴ 60
0
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1
reply
795
views
Comment: Comment: Merging bam files from different runs
18 months ago by shpak.max ▴ 60
1
vote
5
replies
795
views
Merging bam files from different runs
samtools bam
updated 18 months ago by 154k • written 18 months ago by ▴ 60
0
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5
replies
1.7k
views
Stampy make fails
Stampy
updated 20 months ago by • 0 • written 4.2 years ago by ▴ 60
0
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0
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1.3k
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Comment: Comment: Detecting heterozygous deletions in NGS sequence data
2.5 years ago by shpak.max ▴ 60
1
vote
3
replies
1.3k
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Detecting heterozygous deletions in NGS sequence data
fastq vcf GATK
2.5 years ago by shpak.max ▴ 60
0
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1
reply
2.3k
views
Comment: Comment: Read lengths greater than insert length
2.5 years ago by shpak.max ▴ 60
5
votes
3
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2.3k
views
Read lengths greater than insert length
NGS
updated 2.5 years ago by 154k • written 2.5 years ago by ▴ 60
0
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1
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1.3k
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Comment: Comment: Identifying adapter sequence to trim for Illumina IIx data
3.1 years ago by shpak.max ▴ 60
0
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3
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1.3k
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Identifying adapter sequence to trim for Illumina IIx data
trimmomatic
updated 3.1 years ago by 15k • written 3.1 years ago by ▴ 60
0
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0
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2.5k
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Comment: Comment: How does one use rename in seqkit to change sequence labels
3.1 years ago by shpak.max ▴ 60
2
votes
3
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2.5k
views
How does one use rename in seqkit to change sequence labels
seqkit
3.1 years ago by shpak.max ▴ 60
0
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1
reply
2.4k
views
Comment: Comment: Treating forward and reverse reads independently in BWA
3.1 years ago by shpak.max ▴ 60
0
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1
reply
2.4k
views
Comment: Comment: Treating forward and reverse reads independently in BWA
3.1 years ago by shpak.max ▴ 60
0
votes
0
replies
2.4k
views
Comment: Comment: Treating forward and reverse reads independently in BWA
3.1 years ago by shpak.max ▴ 60
0
votes
2
replies
2.4k
views
Comment: Comment: Treating forward and reverse reads independently in BWA
3.1 years ago by shpak.max ▴ 60
1
vote
10
replies
2.4k
views
Treating forward and reverse reads independently in BWA
bwa
updated 3.1 years ago by 103k • written 3.1 years ago by ▴ 60
0
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0
replies
1.3k
views
Comment: Comment: Sampling short reads from a library with long reads
3.1 years ago by shpak.max ▴ 60
0
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2
replies
1.3k
views
Sampling short reads from a library with long reads
alignments bwa
3.1 years ago by shpak.max ▴ 60
0
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0
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2.0k
views
Comment: Comment: fastq-dump throws "connection failed" error
3.3 years ago by shpak.max ▴ 60
0
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2
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2.0k
views
fastq-dump throws "connection failed" error
SRA fastq fastq-dump
3.3 years ago by shpak.max ▴ 60
1
vote
0
replies
569
views
Identifying/filtering pairwise IBD regions in diploid genomes
IBD
3.6 years ago by shpak.max ▴ 60
0
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0
replies
3.5k
views
Comment: Comment: Using IndexFeatureFile to index vcf
3.8 years ago by shpak.max ▴ 60
2
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2
replies
3.5k
views
Using IndexFeatureFile to index vcf
GATK
3.8 years ago by shpak.max ▴ 60
0
votes
0
replies
1.3k
views
Comment: Comment: Comparing SNP coordinates from alignments to different reference genomes
3.9 years ago by shpak.max ▴ 60
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