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0
votes
0
replies
571
views
Comment:
Comment: Detecting heterozygous deletions in NGS sequence data
5 months ago by
shpak.max
▴ 40
1
vote
3
replies
571
views
Detecting heterozygous deletions in NGS sequence data
fastq
vcf
GATK
5 months ago by
shpak.max
▴ 40
0
votes
1
reply
421
views
Comment:
Comment: Read lengths greater than insert length
6 months ago by
shpak.max
▴ 40
5
votes
3
replies
421
views
Read lengths greater than insert length
NGS
updated 6 months ago by
GenoMax
134k • written 6 months ago by
shpak.max
▴ 40
0
votes
1
reply
599
views
Comment:
Comment: Identifying adapter sequence to trim for Illumina IIx data
12 months ago by
shpak.max
▴ 40
0
votes
3
replies
599
views
Identifying adapter sequence to trim for Illumina IIx data
trimmomatic
updated 12 months ago by
swbarnes2
13k • written 12 months ago by
shpak.max
▴ 40
0
votes
0
replies
723
views
Comment:
Comment: How does one use rename in seqkit to change sequence labels
12 months ago by
shpak.max
▴ 40
2
votes
3
replies
723
views
How does one use rename in seqkit to change sequence labels
seqkit
12 months ago by
shpak.max
▴ 40
0
votes
1
reply
1.2k
views
Comment:
Comment: Treating forward and reverse reads independently in BWA
12 months ago by
shpak.max
▴ 40
0
votes
1
reply
1.2k
views
Comment:
Comment: Treating forward and reverse reads independently in BWA
12 months ago by
shpak.max
▴ 40
0
votes
0
replies
1.2k
views
Comment:
Comment: Treating forward and reverse reads independently in BWA
12 months ago by
shpak.max
▴ 40
0
votes
2
replies
1.2k
views
Comment:
Comment: Treating forward and reverse reads independently in BWA
12 months ago by
shpak.max
▴ 40
1
vote
10
replies
1.2k
views
Treating forward and reverse reads independently in BWA
bwa
updated 12 months ago by
Istvan Albert
98k • written 12 months ago by
shpak.max
▴ 40
0
votes
0
replies
425
views
Comment:
Comment: Sampling short reads from a library with long reads
13 months ago by
shpak.max
▴ 40
0
votes
2
replies
425
views
Sampling short reads from a library with long reads
alignments
bwa
13 months ago by
shpak.max
▴ 40
0
votes
0
replies
1.2k
views
Comment:
Comment: fastq-dump throws "connection failed" error
15 months ago by
shpak.max
▴ 40
0
votes
2
replies
1.2k
views
fastq-dump throws "connection failed" error
SRA
fastq
fastq-dump
15 months ago by
shpak.max
▴ 40
1
vote
0
replies
261
views
Identifying/filtering pairwise IBD regions in diploid genomes
IBD
19 months ago by
shpak.max
▴ 40
0
votes
0
replies
1.8k
views
Comment:
Comment: Using IndexFeatureFile to index vcf
22 months ago by
shpak.max
▴ 40
2
votes
2
replies
1.8k
views
Using IndexFeatureFile to index vcf
GATK
22 months ago by
shpak.max
▴ 40
0
votes
0
replies
764
views
Comment:
Comment: Comparing SNP coordinates from alignments to different reference genomes
22 months ago by
shpak.max
▴ 40
0
votes
2
replies
764
views
Comparing SNP coordinates from alignments to different reference genomes
Samtools
22 months ago by
shpak.max
▴ 40
0
votes
0
replies
1.4k
views
Comment:
Comment: SAM Validation Error with CleanSam (Aligment start must be <= reference seq len
23 months ago by
shpak.max
▴ 40
0
votes
1
reply
1.4k
views
Comment:
Comment: SAM Validation Error with CleanSam (Aligment start must be <= reference seq len
23 months ago by
shpak.max
▴ 40
0
votes
2
replies
1.4k
views
Comment:
Comment: SAM Validation Error with CleanSam (Aligment start must be <= reference seq len
23 months ago by
shpak.max
▴ 40
1
vote
7
replies
1.4k
views
SAM Validation Error with CleanSam (Aligment start must be <= reference seq length)
Samtools
Picard
23 months ago by
shpak.max
▴ 40
0
votes
0
replies
346
views
Using PoolSNP to return non-SNP genotypes
PoolSNP
23 months ago by
shpak.max
▴ 40
0
votes
0
replies
359
views
Using UnifiedGenotyper on single chromosome without coordinates
GATK
2.0 years ago by
shpak.max
▴ 40
0
votes
1
reply
872
views
Comment:
Comment: Genotyping low read depth sequences using GATK
2.1 years ago by
shpak.max
▴ 40
0
votes
3
replies
872
views
Genotyping low read depth sequences using GATK
GATK
updated 2.1 years ago by
vdauwera
★ 1.2k • written 2.1 years ago by
shpak.max
▴ 40
0
votes
0
replies
5.0k
views
Comment:
Comment: bcftools consensus still returns "Could not parse the header" error
2.1 years ago by
shpak.max
▴ 40
0
votes
2
replies
5.0k
views
Comment:
Comment: bcftools consensus still returns "Could not parse the header" error
2.1 years ago by
shpak.max
▴ 40
0
votes
5
replies
5.0k
views
bcftools consensus still returns "Could not parse the header" error
bcftools
samtools
2.1 years ago by
shpak.max
▴ 40
0
votes
1
reply
3.5k
views
Comment:
Comment: Probable bug in bcftools while parsing headers
2.1 years ago by
shpak.max
▴ 40
0
votes
0
replies
305
views
PoolSNP RuntimeError: dictionary changed size during iteration
Poolsnp
2.2 years ago by
shpak.max
▴ 40
0
votes
1
reply
1.2k
views
bamdst gives error "EOF marker is absent. The input is probably truncated."
bwa
samtools
bamdst
updated 2.0 years ago by
aw7
▴ 210 • written 2.2 years ago by
shpak.max
▴ 40
0
votes
1
reply
913
views
Comment:
Comment: Troubleshooting Missing_Read_Group and Mismatch_Flag_Mate Errors
2.2 years ago by
shpak.max
▴ 40
1
vote
3
replies
913
views
Troubleshooting Missing_Read_Group and Mismatch_Flag_Mate Errors
Picard
BWA
updated 2.2 years ago by
GenoMax
134k • written 2.2 years ago by
shpak.max
▴ 40
0
votes
1
reply
2.8k
views
Comment:
Comment: Input arguments for AddOrReplaceReadGroups (Picard) from fastq
2.2 years ago by
shpak.max
▴ 40
3
votes
3
replies
2.8k
views
Input arguments for AddOrReplaceReadGroups (Picard) from fastq
Picard
GATK
updated 2.2 years ago by
vdauwera
★ 1.2k • written 2.2 years ago by
shpak.max
▴ 40
0
votes
0
replies
770
views
Comment:
Comment: Stampy make fails
2.2 years ago by
shpak.max
▴ 40
0
votes
1
reply
770
views
Comment:
Comment: Stampy make fails
2.2 years ago by
shpak.max
▴ 40
0
votes
4
replies
770
views
Stampy make fails
Stampy
2.2 years ago by
shpak.max
▴ 40
0
votes
1
reply
553
views
Comment:
Comment: Why split fastq files?
2.2 years ago by
shpak.max
▴ 40
2
votes
3
replies
553
views
Why split fastq files?
fastq
alignments
ngs
bwa
updated 2.2 years ago by
GenoMax
134k • written 2.2 years ago by
shpak.max
▴ 40
0
votes
0
replies
539
views
Input arguments to list ancestral sequences in emboss phylip (dnapars)
Emboss
phylip
updated 2.9 years ago by
Biostar
20 • written 3.1 years ago by
shpak.max
▴ 40
0
votes
0
replies
2.7k
views
minimum information content in .maf to run mutsig
MutSig
updated 3.1 years ago by
Biostar
20 • written 8.9 years ago by
shpak.max
▴ 40
0
votes
0
replies
1.6k
views
Comment:
C: EMBOSS program for calculating dN/dS from MSA
3.2 years ago by
shpak.max
▴ 40
1
vote
2
replies
1.6k
views
EMBOSS program for calculating dN/dS from MSA
EMBOSS
updated 3.2 years ago by
Mark
★ 1.3k • written 3.2 years ago by
shpak.max
▴ 40
0
votes
1
reply
1.1k
views
Creating .phy files in clustal without truncation
clustal
phylip
updated 3.2 years ago by
Mensur Dlakic
★ 24k • written 3.2 years ago by
shpak.max
▴ 40
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