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0
votes
2
replies
1.2k
views
Remove polymorphic SNPs from VCF file
SNP
updated 2.0 years ago by • 0 • written 4.0 years ago by ▴ 60
7
votes
5
replies
3.6k
views
How to annotate eukaryotic genome
Assembly genome
updated 2.3 years ago by ▴ 110 • written 4.1 years ago by ▴ 60
0
votes
1
reply
714
views
Get corresponding SRA accessions for very large list of Biosample accesions?
NCBI Enterez direct
updated 2.6 years ago by 142k • written 2.6 years ago by ▴ 60
0
votes
1
reply
897
views
Pan-genome visualization similar to anvio?
analysis pangenome
updated 2.6 years ago by 3.6k • written 2.6 years ago by ▴ 60
0
votes
0
replies
418
views
How to deal with differences in sample size for metagenomic diversity based on abundance?
metagenomics sample-size
updated 13 months ago by 43k • written 2.7 years ago by ▴ 60
0
votes
1
reply
474
views
combine metagenomic assemblies using cat?
Assembly
updated 2.9 years ago by 3.6k • written 2.9 years ago by ▴ 60
0
votes
4
replies
1.5k
views
remove variable sites from vcf that only differ from reference.
vcf
updated 3.1 years ago by ▴ 130 • written 3.1 years ago by ▴ 60
1
vote
2
replies
800
views
how to align sequences in multifasta
alignment
updated 3.1 years ago by 142k • written 3.1 years ago by ▴ 60
0
votes
1
reply
470
views
tool for visualizing small sets of genes
sequence gene
3.2 years ago by goatsrunfaster ▴ 60
0
votes
0
replies
390
views
predict genes in set of eukaryotic DNA contigs?
gene
3.2 years ago by goatsrunfaster ▴ 60
0
votes
0
replies
583
views
filter haploid SNP data for use with STRUCTURE
SNP
3.3 years ago by goatsrunfaster ▴ 60
0
votes
1
reply
1.0k
views
Get corresponding Biosample accessions for very large list of SRA accesions?
next-gen
updated 3.4 years ago by ★ 3.7k • written 3.4 years ago by ▴ 60
0
votes
1
reply
401
views
blast query using list instead of single .fa files from command line?
alignment sequence
3.4 years ago by goatsrunfaster ▴ 60
0
votes
0
replies
811
views
Comment: C: Convert multi amino acid sequence file (.faa) to nucleotide sequence file (multi
3.5 years ago by goatsrunfaster ▴ 60
1
vote
2
replies
811
views
Convert multi amino acid sequence file (.faa) to nucleotide sequence file (multifasta; .fa)?
alignment
3.5 years ago by goatsrunfaster ▴ 60
0
votes
2
replies
1.0k
views
change duplicate headers to unique headers in multifasta
sequence
updated 3.5 years ago by 82k • written 3.5 years ago by ▴ 60
0
votes
1
reply
535
views
looking for a way to identify a specific gene, and in varying numbers across multiple genomes.
gene
updated 3.6 years ago by ▴ 20 • written 3.6 years ago by ▴ 60
0
votes
1
reply
787
views
Problems setting up nt blast database
software error
3.6 years ago by goatsrunfaster ▴ 60
0
votes
0
replies
787
views
Answer: A: Problems setting up nt blast database
3.6 years ago by goatsrunfaster ▴ 60
3
votes
8
replies
5.1k
views
extract single contig from fasta file based on name?
Assembly
updated 3.6 years ago by ▴ 130 • written 3.6 years ago by ▴ 60
0
votes
0
replies
5.1k
views
Comment: C: extract single contig from fasta file based on name?
3.6 years ago by goatsrunfaster ▴ 60
0
votes
2
replies
5.1k
views
Comment: C: extract single contig from fasta file based on name?
3.6 years ago by goatsrunfaster ▴ 60
0
votes
1
reply
1.0k
views
Comment: A: Looking for easy to use eukaryotic genome annotation pipeline?
3.6 years ago by goatsrunfaster ▴ 60
3
votes
6
replies
1.0k
views
Looking for easy to use eukaryotic genome annotation pipeline?
Assembly
3.6 years ago by goatsrunfaster ▴ 60
1
vote
0
replies
2.0k
views
Answer: A: exclude variants based on position in vcf file
4.0 years ago by goatsrunfaster ▴ 60
1
vote
1
reply
2.0k
views
exclude variants based on position in vcf file
SNP
4.0 years ago by goatsrunfaster ▴ 60
0
votes
0
replies
1.2k
views
Comment: C: Remove polymorphic SNPs from VCF file
4.0 years ago by goatsrunfaster ▴ 60
0
votes
1
reply
741
views
minimum contig size in partial eukaryotic assembly
Assembly genome
updated 4.1 years ago by 13k • written 4.1 years ago by ▴ 60
0
votes
0
replies
3.6k
views
Comment: C: How to annotate eukaryotic genome
4.1 years ago by goatsrunfaster ▴ 60
1
vote
4
replies
1.5k
views
blasting a fasta file with many, many contigs via command line
Assembly genome
updated 4.1 years ago by 6.4k • written 4.1 years ago by ▴ 60
0
votes
0
replies
1.7k
views
Comment: C: Interpreting abyss output
4.1 years ago by goatsrunfaster ▴ 60
2
votes
2
replies
1.7k
views
Interpreting abyss output
Assembly genome
updated 4.2 years ago by 15k • written 4.2 years ago by ▴ 60
1
vote
2
replies
1.1k
views
How to filter multi-VCF for positions that have an SNP (in contrast to the reference) across all samples?
SNP genome sequence
updated 4.3 years ago by 16k • written 4.3 years ago by ▴ 60
0
votes
0
replies
1.6k
views
Comment: C: Identify fixed differences between population in WGS data (VCF Format)
4.3 years ago by goatsrunfaster ▴ 60
0
votes
1
reply
1.6k
views
Comment: C: Identify fixed differences between population in WGS data (VCF Format)
4.3 years ago by goatsrunfaster ▴ 60
1
vote
1
reply
961
views
interpreting assembly contiguity statistics
Assembly sequencing
4.4 years ago by goatsrunfaster ▴ 60
1
vote
2
replies
826
views
Remove variants in VCF with the same call in all but the reference
SNP genome
updated 4.4 years ago by ★ 1.0k • written 4.4 years ago by ▴ 60
4
votes
3
replies
1.6k
views
Identify fixed differences between population in WGS data (VCF Format)
SNP genome next-gen
updated 4.4 years ago by ★ 3.8k • written 4.4 years ago by ▴ 60
0
votes
0
replies
891
views
Comment: C: Using SnpSift to filter VCF for protein_coding regions not working
4.4 years ago by goatsrunfaster ▴ 60
0
votes
1
reply
891
views
Comment: C: Using SnpSift to filter VCF for protein_coding regions not working
4.4 years ago by goatsrunfaster ▴ 60
0
votes
3
replies
891
views
Using SnpSift to filter VCF for protein_coding regions not working
SNP genome next-gen
4.4 years ago by goatsrunfaster ▴ 60
0
votes
0
replies
1.2k
views
Comment: C: How to filter .vcf based on .gbk file to remove SNP calls in non-CDS regions?
4.4 years ago by goatsrunfaster ▴ 60
4
votes
2
replies
1.2k
views
How to filter .vcf based on .gbk file to remove SNP calls in non-CDS regions?
SNP genome
updated 4.4 years ago by 161k • written 4.4 years ago by ▴ 60
1
vote
1
reply
3.0k
views
FORMAT 'PL' is not defined in the header, assuming Type=String (bcftools)
snp vcf
updated 4.9 years ago by 43k • written 4.9 years ago by ▴ 60
3
votes
5
replies
2.7k
views
Merge VCF files with diploid reference calls in different order for same positions (e.g. TC vs CT)
snp vcf
updated 4.9 years ago by 16k • written 4.9 years ago by ▴ 60
0
votes
0
replies
2.7k
views
Comment: C: Merge VCF files with diploid reference calls in different order for same positio
4.9 years ago by goatsrunfaster ▴ 60
0
votes
1
reply
2.7k
views
Comment: C: Merge VCF files with diploid reference calls in different order for same positio
4.9 years ago by goatsrunfaster ▴ 60
0
votes
0
replies
534
views
Identify unique SNPs specific to pre-defined clades or clusters across large data-set
SNP genome alignment
5.3 years ago by goatsrunfaster ▴ 60
1
vote
1
reply
1.7k
views
Lositan, He and Microsats (expected heterozygosity measures plot higher than expected)
Lositan Expected Heterozygosity Microsatellites
7.9 years ago by goatsrunfaster ▴ 60
1
vote
0
replies
1.7k
views
Answer: A: Lositan, He and Microsats (expected heterozygosity measures plot higher than exp
7.9 years ago by goatsrunfaster ▴ 60
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