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0
votes
2
replies
1.6k
views
Remove polymorphic SNPs from VCF file
SNP
updated 3.4 years ago by • 0 • written 5.4 years ago by ▴ 60
7
votes
6
replies
6.5k
views
How to annotate eukaryotic genome
Assembly genome
updated 14 months ago by 9.3k • written 5.6 years ago by ▴ 60
0
votes
1
reply
1.1k
views
Get corresponding SRA accessions for very large list of Biosample accesions?
NCBI Enterez direct
updated 4.0 years ago by 154k • written 4.0 years ago by ▴ 60
0
votes
1
reply
1.3k
views
Pan-genome visualization similar to anvio?
analysis pangenome
updated 4.1 years ago by 3.9k • written 4.1 years ago by ▴ 60
0
votes
0
replies
600
views
How to deal with differences in sample size for metagenomic diversity based on abundance?
metagenomics sample-size
updated 2.5 years ago by 45k • written 4.1 years ago by ▴ 60
0
votes
1
reply
722
views
combine metagenomic assemblies using cat?
Assembly
updated 4.3 years ago by 3.9k • written 4.3 years ago by ▴ 60
0
votes
4
replies
2.5k
views
remove variable sites from vcf that only differ from reference.
vcf
updated 4.5 years ago by ▴ 170 • written 4.5 years ago by ▴ 60
1
vote
2
replies
1.1k
views
how to align sequences in multifasta
alignment
updated 4.5 years ago by 154k • written 4.5 years ago by ▴ 60
0
votes
1
reply
708
views
tool for visualizing small sets of genes
sequence gene
4.6 years ago by goatsrunfaster ▴ 60
0
votes
0
replies
580
views
predict genes in set of eukaryotic DNA contigs?
gene
4.7 years ago by goatsrunfaster ▴ 60
0
votes
0
replies
763
views
filter haploid SNP data for use with STRUCTURE
SNP
4.7 years ago by goatsrunfaster ▴ 60
0
votes
1
reply
1.4k
views
Get corresponding Biosample accessions for very large list of SRA accesions?
next-gen
updated 4.8 years ago by ★ 3.9k • written 4.8 years ago by ▴ 60
0
votes
1
reply
597
views
blast query using list instead of single .fa files from command line?
alignment sequence
4.9 years ago by goatsrunfaster ▴ 60
0
votes
0
replies
1.3k
views
Comment: C: Convert multi amino acid sequence file (.faa) to nucleotide sequence file (multi
4.9 years ago by goatsrunfaster ▴ 60
1
vote
2
replies
1.3k
views
Convert multi amino acid sequence file (.faa) to nucleotide sequence file (multifasta; .fa)?
alignment
4.9 years ago by goatsrunfaster ▴ 60
0
votes
2
replies
1.3k
views
change duplicate headers to unique headers in multifasta
sequence
updated 4.9 years ago by 89k • written 4.9 years ago by ▴ 60
0
votes
1
reply
768
views
looking for a way to identify a specific gene, and in varying numbers across multiple genomes.
gene
updated 5.0 years ago by ▴ 20 • written 5.0 years ago by ▴ 60
0
votes
0
replies
1.1k
views
Answer: A: Problems setting up nt blast database
5.0 years ago by goatsrunfaster ▴ 60
0
votes
1
reply
1.1k
views
Problems setting up nt blast database
software error
5.0 years ago by goatsrunfaster ▴ 60
3
votes
8
replies
7.8k
views
extract single contig from fasta file based on name?
Assembly
updated 5.0 years ago by ▴ 130 • written 5.0 years ago by ▴ 60
0
votes
0
replies
7.8k
views
Comment: C: extract single contig from fasta file based on name?
5.0 years ago by goatsrunfaster ▴ 60
0
votes
2
replies
7.8k
views
Comment: C: extract single contig from fasta file based on name?
5.0 years ago by goatsrunfaster ▴ 60
3
votes
6
replies
1.7k
views
Looking for easy to use eukaryotic genome annotation pipeline?
Assembly
5.0 years ago by goatsrunfaster ▴ 60
0
votes
1
reply
1.7k
views
Comment: A: Looking for easy to use eukaryotic genome annotation pipeline?
5.0 years ago by goatsrunfaster ▴ 60
1
vote
0
replies
2.4k
views
Answer: A: exclude variants based on position in vcf file
5.4 years ago by goatsrunfaster ▴ 60
1
vote
1
reply
2.4k
views
exclude variants based on position in vcf file
SNP
5.4 years ago by goatsrunfaster ▴ 60
0
votes
0
replies
1.6k
views
Comment: C: Remove polymorphic SNPs from VCF file
5.4 years ago by goatsrunfaster ▴ 60
0
votes
1
reply
1.0k
views
minimum contig size in partial eukaryotic assembly
Assembly genome
updated 5.6 years ago by 13k • written 5.6 years ago by ▴ 60
0
votes
0
replies
6.5k
views
Comment: C: How to annotate eukaryotic genome
5.6 years ago by goatsrunfaster ▴ 60
1
vote
4
replies
2.8k
views
blasting a fasta file with many, many contigs via command line
Assembly genome
updated 5.6 years ago by 8.0k • written 5.6 years ago by ▴ 60
0
votes
0
replies
2.6k
views
Comment: C: Interpreting abyss output
5.6 years ago by goatsrunfaster ▴ 60
2
votes
2
replies
2.6k
views
Interpreting abyss output
Assembly genome
updated 5.6 years ago by 16k • written 5.6 years ago by ▴ 60
1
vote
2
replies
1.4k
views
How to filter multi-VCF for positions that have an SNP (in contrast to the reference) across all samples?
SNP genome sequence
updated 5.7 years ago by 16k • written 5.7 years ago by ▴ 60
0
votes
0
replies
2.4k
views
Comment: C: Identify fixed differences between population in WGS data (VCF Format)
5.7 years ago by goatsrunfaster ▴ 60
0
votes
1
reply
2.4k
views
Comment: C: Identify fixed differences between population in WGS data (VCF Format)
5.7 years ago by goatsrunfaster ▴ 60
1
vote
1
reply
1.2k
views
interpreting assembly contiguity statistics
Assembly sequencing
5.8 years ago by goatsrunfaster ▴ 60
1
vote
2
replies
1.2k
views
Remove variants in VCF with the same call in all but the reference
SNP genome
updated 5.8 years ago by ★ 1.0k • written 5.8 years ago by ▴ 60
4
votes
3
replies
2.4k
views
Identify fixed differences between population in WGS data (VCF Format)
SNP genome next-gen
updated 5.8 years ago by ★ 3.8k • written 5.8 years ago by ▴ 60
0
votes
0
replies
1.4k
views
Comment: C: Using SnpSift to filter VCF for protein_coding regions not working
5.8 years ago by goatsrunfaster ▴ 60
0
votes
1
reply
1.4k
views
Comment: C: Using SnpSift to filter VCF for protein_coding regions not working
5.8 years ago by goatsrunfaster ▴ 60
0
votes
3
replies
1.4k
views
Using SnpSift to filter VCF for protein_coding regions not working
SNP genome next-gen
5.8 years ago by goatsrunfaster ▴ 60
0
votes
0
replies
1.7k
views
Comment: C: How to filter .vcf based on .gbk file to remove SNP calls in non-CDS regions?
5.8 years ago by goatsrunfaster ▴ 60
4
votes
2
replies
1.7k
views
How to filter .vcf based on .gbk file to remove SNP calls in non-CDS regions?
SNP genome
updated 5.8 years ago by 166k • written 5.8 years ago by ▴ 60
1
vote
1
reply
3.5k
views
FORMAT 'PL' is not defined in the header, assuming Type=String (bcftools)
snp vcf
updated 6.3 years ago by 45k • written 6.3 years ago by ▴ 60
3
votes
5
replies
3.6k
views
Merge VCF files with diploid reference calls in different order for same positions (e.g. TC vs CT)
snp vcf
updated 6.3 years ago by 16k • written 6.3 years ago by ▴ 60
0
votes
0
replies
3.6k
views
Comment: C: Merge VCF files with diploid reference calls in different order for same positio
6.3 years ago by goatsrunfaster ▴ 60
0
votes
1
reply
3.6k
views
Comment: C: Merge VCF files with diploid reference calls in different order for same positio
6.3 years ago by goatsrunfaster ▴ 60
0
votes
0
replies
721
views
Identify unique SNPs specific to pre-defined clades or clusters across large data-set
SNP genome alignment
6.7 years ago by goatsrunfaster ▴ 60
1
vote
1
reply
2.0k
views
Lositan, He and Microsats (expected heterozygosity measures plot higher than expected)
Lositan Expected Heterozygosity Microsatellites
9.3 years ago by goatsrunfaster ▴ 60
1
vote
0
replies
2.0k
views
Answer: A: Lositan, He and Microsats (expected heterozygosity measures plot higher than exp
9.3 years ago by goatsrunfaster ▴ 60
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