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0
votes
2
replies
1.9k
views
Comment:
Comment: How could I "recreate" UniRef50/UniRef90 with MMSEQS2?
14 months ago by
O.rka
▴ 710
1
vote
4
replies
1.9k
views
How could I "recreate" UniRef50/UniRef90 with MMSEQS2?
clustering
proteins
annotation
mmseqs2
updated 9 months ago by
Zachary
• 0 • written 14 months ago by
O.rka
▴ 710
1
vote
2
replies
1.9k
views
Are there any tools that can create a very basic GTF file from contig sequences (no annotations really needed) ?
Assembly
mapping
14 months ago by
O.rka
▴ 710
0
votes
0
replies
1.9k
views
Answer:
Answer: Are there any tools that can create a very basic GTF file from contig sequences
14 months ago by
O.rka
▴ 710
0
votes
0
replies
373
views
What's the state-of-the-art for gene calling in eukaryotic transcriptomics?
modeling
eukaryotic
transcriptomics
call
gene
15 months ago by
O.rka
▴ 710
0
votes
1
reply
1.1k
views
Comment:
Comment: How can I run multiple sequence alignment for a large number of proteins (~10k)
15 months ago by
O.rka
▴ 710
3
votes
5
replies
1.1k
views
How can I run multiple sequence alignment for a large number of proteins (~10k)
muscle
msa
protein
multiple
alignment
sequence
updated 15 months ago by
Mensur Dlakic
★ 27k • written 15 months ago by
O.rka
▴ 710
0
votes
0
replies
1.1k
views
Comment:
Comment: How can I run multiple sequence alignment for a large number of proteins (~10k)
15 months ago by
O.rka
▴ 710
0
votes
0
replies
1.4k
views
Comment:
Comment: Any command line tools that can design primers from a multiple sequence alignmen
16 months ago by
O.rka
▴ 710
0
votes
1
reply
1.4k
views
Comment:
Comment: Any command line tools that can design primers from a multiple sequence alignmen
16 months ago by
O.rka
▴ 710
0
votes
0
replies
642
views
Comment:
Comment: What's best practice when determining a degenerate base when creating a primer?
16 months ago by
O.rka
▴ 710
1
vote
2
replies
642
views
What's best practice when determining a degenerate base when creating a primer?
primer-design
alignment
genomics
16 months ago by
O.rka
▴ 710
0
votes
1
reply
1.4k
views
Comment:
Comment: Any command line tools that can design primers from a multiple sequence alignmen
16 months ago by
O.rka
▴ 710
1
vote
6
replies
1.4k
views
Any command line tools that can design primers from a multiple sequence alignment?
primer-design
genomics
cli
16 months ago by
O.rka
▴ 710
0
votes
1
reply
1.5k
views
Comment:
Comment: What in silico PCR commandline tool do you use that can handle IUPAC characters?
16 months ago by
O.rka
▴ 710
1
vote
1
reply
1.5k
views
Comment:
Comment: What in silico PCR commandline tool do you use that can handle IUPAC characters?
16 months ago by
O.rka
▴ 710
0
votes
0
replies
70k
views
Comment:
Comment: Sequence length from Fasta
16 months ago by
O.rka
▴ 710
9
votes
6
replies
1.5k
views
What in silico PCR commandline tool do you use that can handle IUPAC characters?
pcr
amplicon
primer
updated 4 weeks ago by
Ram
43k • written 16 months ago by
O.rka
▴ 710
0
votes
0
replies
776
views
Comment:
Comment: How to find full length ribosomal sequences for fungi?
16 months ago by
O.rka
▴ 710
3
votes
3
replies
776
views
How to find full length ribosomal sequences for fungi?
ncbi
ribosomal
fungi
nt
16 months ago by
O.rka
▴ 710
0
votes
0
replies
323
views
How to estimate the memory requirements for Diamond given the database and query protein sizes?
alignment
diamond
memory
requirements
16 months ago by
O.rka
▴ 710
0
votes
0
replies
685
views
Comment:
Comment: How to "enrich" a large set of proteins (>11M) for protein hits in UniRef90?
16 months ago by
O.rka
▴ 710
0
votes
1
reply
685
views
Comment:
Comment: How to "enrich" a large set of proteins (>11M) for protein hits in UniRef90?
16 months ago by
O.rka
▴ 710
0
votes
4
replies
685
views
How to "enrich" a large set of proteins (>11M) for protein hits in UniRef90?
uniref
proteins
alignment
16 months ago by
O.rka
▴ 710
0
votes
0
replies
1.3k
views
Comment:
Comment: How to extract unmapped reads if you have paired end reads (fastq) and mapped BA
18 months ago by
O.rka
▴ 710
0
votes
1
reply
1.3k
views
Comment:
Comment: How to extract unmapped reads if you have paired end reads (fastq) and mapped BA
18 months ago by
O.rka
▴ 710
3
votes
4
replies
1.3k
views
How to extract unmapped reads if you have paired end reads (fastq) and mapped BAM file?
fastq
bam
sam
reads
18 months ago by
O.rka
▴ 710
2
votes
2
replies
868
views
What's the benefit of using the `no_alt_analysis_set` Bowtie2 index over the primary assembly?
human
rnaseq
mapping
metagenomics
updated 18 months ago by
ATpoint
82k • written 18 months ago by
O.rka
▴ 710
0
votes
1
reply
678
views
Is there a tool that quantifies “spatial coverage”, that is what percentage of a reference assembly has a read mapped to it?
coverage
genomics
mapping
assembly
updated 20 months ago by
GenoMax
142k • written 20 months ago by
O.rka
▴ 710
0
votes
0
replies
1.6k
views
Comment:
Comment: Are there any tools that automatically detect where to truncate forward and reve
21 months ago by
O.rka
▴ 710
0
votes
0
replies
550
views
Comment:
Comment: How to calculate position-specific fastq stats?
21 months ago by
O.rka
▴ 710
0
votes
2
replies
550
views
How to calculate position-specific fastq stats?
rnaseq
fastq
metagenomics
genomics
21 months ago by
O.rka
▴ 710
0
votes
3
replies
1.6k
views
Are there any tools that automatically detect where to truncate forward and reverse reads for 16S (DADA2)?
16s
dada2
illumina
metagenomics
qiime2
21 months ago by
O.rka
▴ 710
0
votes
1
reply
1.2k
views
Comment:
Comment: Is it required for all sequences to be same length when clustering OTUs in metag
21 months ago by
O.rka
▴ 710
1
vote
3
replies
1.2k
views
Is it required for all sequences to be same length when clustering OTUs in metagenomics (ONT Nanopore)
otu
metagenomics
clustering
nanopore
updated 21 months ago by
antonioggsousa
3.2k • written 21 months ago by
O.rka
▴ 710
0
votes
0
replies
629
views
Comment:
Comment: What percent identity is recommended for detecting protein homology within a spe
21 months ago by
O.rka
▴ 710
0
votes
2
replies
629
views
What percent identity is recommended for detecting protein homology within a species?
alignment
genomics
proteomics
21 months ago by
O.rka
▴ 710
0
votes
0
replies
1.6k
views
Comment:
Comment: Is there a tool that calculates genome coverage? (e.g., 1X, 10X, 100X)
22 months ago by
O.rka
▴ 710
0
votes
1
reply
1.6k
views
Comment:
Comment: Is there a tool that calculates genome coverage? (e.g., 1X, 10X, 100X)
22 months ago by
O.rka
▴ 710
0
votes
1
reply
1.6k
views
Comment:
Comment: Is there a tool that calculates genome coverage? (e.g., 1X, 10X, 100X)
22 months ago by
O.rka
▴ 710
1
vote
6
replies
1.6k
views
Is there a tool that calculates genome coverage? (e.g., 1X, 10X, 100X)
ncbi
metagenomics
submission
22 months ago by
O.rka
▴ 710
0
votes
1
reply
477
views
Software to produce position-specific conservation of multiple sequence alignment results?
transcriptomics
genomics
alignment
proteomics
updated 22 months ago by
Mensur Dlakic
★ 27k • written 22 months ago by
O.rka
▴ 710
0
votes
1
reply
1.0k
views
How to count the number of multimapped reads from a bam file?
rnaseq
mapping
bowtie2
featurecounts
updated 22 months ago by
Shred
★ 1.4k • written 22 months ago by
O.rka
▴ 710
1
vote
1
reply
928
views
Advice on mapping reads to polyploid de-novo assembly
assembly
RNA-Seq
updated 23 months ago by
colindaven
6.4k • written 4.3 years ago by
O.rka
▴ 710
0
votes
1
reply
579
views
How do you predict regions on a protein that are exposed on the cell surface?
protein
antibody
hmm
domain
updated 23 months ago by
Mensur Dlakic
★ 27k • written 23 months ago by
O.rka
▴ 710
0
votes
0
replies
966
views
Comment:
Comment: How can I get a taxid from an assembly id (e.g., GCA_003223415.1 -> 2026742)
24 months ago by
O.rka
▴ 710
3
votes
2
replies
966
views
How can I get a taxid from an assembly id (e.g., GCA_003223415.1 -> 2026742)
metagenomics
accession
ncbi
taxonomy
database
24 months ago by
O.rka
▴ 710
3
votes
1
reply
645
views
What are the suggested parameters for running IQ-TREE on a protein alignment for phylogeny?
protein
metagenomics
phylogeny
iqtree
updated 2.0 years ago by
Mensur Dlakic
★ 27k • written 2.0 years ago by
O.rka
▴ 710
0
votes
1
reply
4.1k
views
Comment:
Comment: What are the recommended methods for merging de-novo assemblies?
2.0 years ago by
O.rka
▴ 710
0
votes
0
replies
465
views
Does anyone know how to filter by strategy on NCBI's search in BioProject/SRA? (e.g., no amplicons)
search
metagenomics
sra
ncbi
meta
2.1 years ago by
O.rka
▴ 710
408 results • Page
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