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Comment: Comment: How could I "recreate" UniRef50/UniRef90 with MMSEQS2?
14 months ago by O.rka ▴ 720
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4
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How could I "recreate" UniRef50/UniRef90 with MMSEQS2?
clustering proteins annotation mmseqs2
updated 9 months ago by • 0 • written 14 months ago by ▴ 720
1
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2
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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 ▴ 720
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0
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1.9k
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Answer: Answer: Are there any tools that can create a very basic GTF file from contig sequences
14 months ago by O.rka ▴ 720
0
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0
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375
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What's the state-of-the-art for gene calling in eukaryotic transcriptomics?
modeling eukaryotic transcriptomics call gene
15 months ago by O.rka ▴ 720
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1
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1.1k
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Comment: Comment: How can I run multiple sequence alignment for a large number of proteins (~10k)
16 months ago by O.rka ▴ 720
3
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5
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1.1k
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How can I run multiple sequence alignment for a large number of proteins (~10k)
muscle msa protein multiple alignment sequence
updated 16 months ago by ★ 27k • written 16 months ago by ▴ 720
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0
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1.1k
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Comment: Comment: How can I run multiple sequence alignment for a large number of proteins (~10k)
16 months ago by O.rka ▴ 720
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0
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1.4k
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Comment: Comment: Any command line tools that can design primers from a multiple sequence alignmen
16 months ago by O.rka ▴ 720
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1
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1.4k
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Comment: Comment: Any command line tools that can design primers from a multiple sequence alignmen
16 months ago by O.rka ▴ 720
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0
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643
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Comment: Comment: What's best practice when determining a degenerate base when creating a primer?
16 months ago by O.rka ▴ 720
1
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2
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643
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What's best practice when determining a degenerate base when creating a primer?
primer-design alignment genomics
16 months ago by O.rka ▴ 720
0
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1
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1.4k
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Comment: Comment: Any command line tools that can design primers from a multiple sequence alignmen
16 months ago by O.rka ▴ 720
1
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6
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1.4k
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Any command line tools that can design primers from a multiple sequence alignment?
primer-design genomics cli
16 months ago by O.rka ▴ 720
0
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1
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1.5k
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Comment: Comment: What in silico PCR commandline tool do you use that can handle IUPAC characters?
16 months ago by O.rka ▴ 720
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1
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1.5k
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Comment: Comment: What in silico PCR commandline tool do you use that can handle IUPAC characters?
16 months ago by O.rka ▴ 720
0
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0
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70k
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Comment: Comment: Sequence length from Fasta
16 months ago by O.rka ▴ 720
9
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6
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1.5k
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What in silico PCR commandline tool do you use that can handle IUPAC characters?
pcr amplicon primer
updated 5 weeks ago by 43k • written 16 months ago by ▴ 720
0
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0
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779
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Comment: Comment: How to find full length ribosomal sequences for fungi?
16 months ago by O.rka ▴ 720
3
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3
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779
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How to find full length ribosomal sequences for fungi?
ncbi ribosomal fungi nt
16 months ago by O.rka ▴ 720
0
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0
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323
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How to estimate the memory requirements for Diamond given the database and query protein sizes?
alignment diamond memory requirements
17 months ago by O.rka ▴ 720
0
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0
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685
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Comment: Comment: How to "enrich" a large set of proteins (>11M) for protein hits in UniRef90?
17 months ago by O.rka ▴ 720
0
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1
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685
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Comment: Comment: How to "enrich" a large set of proteins (>11M) for protein hits in UniRef90?
17 months ago by O.rka ▴ 720
0
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4
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685
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How to "enrich" a large set of proteins (>11M) for protein hits in UniRef90?
uniref proteins alignment
17 months ago by O.rka ▴ 720
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0
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1.3k
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Comment: Comment: How to extract unmapped reads if you have paired end reads (fastq) and mapped BA
18 months ago by O.rka ▴ 720
0
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1
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1.3k
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Comment: Comment: How to extract unmapped reads if you have paired end reads (fastq) and mapped BA
18 months ago by O.rka ▴ 720
3
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4
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1.3k
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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 ▴ 720
2
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2
replies
874
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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 82k • written 18 months ago by ▴ 720
0
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1
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678
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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 21 months ago by 142k • written 21 months ago by ▴ 720
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0
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1.7k
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Comment: Comment: Are there any tools that automatically detect where to truncate forward and reve
21 months ago by O.rka ▴ 720
0
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0
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553
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Comment: Comment: How to calculate position-specific fastq stats?
21 months ago by O.rka ▴ 720
0
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2
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553
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How to calculate position-specific fastq stats?
rnaseq fastq metagenomics genomics
21 months ago by O.rka ▴ 720
0
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3
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1.7k
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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 ▴ 720
0
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1
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1.2k
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Comment: Comment: Is it required for all sequences to be same length when clustering OTUs in metag
21 months ago by O.rka ▴ 720
1
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3
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1.2k
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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 3.2k • written 21 months ago by ▴ 720
0
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0
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631
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Comment: Comment: What percent identity is recommended for detecting protein homology within a spe
21 months ago by O.rka ▴ 720
0
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2
replies
631
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What percent identity is recommended for detecting protein homology within a species?
alignment genomics proteomics
21 months ago by O.rka ▴ 720
0
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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 ▴ 720
0
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1
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1.6k
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Comment: Comment: Is there a tool that calculates genome coverage? (e.g., 1X, 10X, 100X)
22 months ago by O.rka ▴ 720
0
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1
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1.6k
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Comment: Comment: Is there a tool that calculates genome coverage? (e.g., 1X, 10X, 100X)
22 months ago by O.rka ▴ 720
1
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6
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1.6k
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Is there a tool that calculates genome coverage? (e.g., 1X, 10X, 100X)
ncbi metagenomics submission
22 months ago by O.rka ▴ 720
0
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1
reply
478
views
Software to produce position-specific conservation of multiple sequence alignment results?
transcriptomics genomics alignment proteomics
updated 22 months ago by ★ 27k • written 22 months ago by ▴ 720
0
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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 ★ 1.4k • written 22 months ago by ▴ 720
1
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1
reply
928
views
Advice on mapping reads to polyploid de-novo assembly
assembly RNA-Seq
updated 23 months ago by 6.4k • written 4.3 years ago by ▴ 720
0
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1
reply
582
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 ★ 27k • written 23 months ago by ▴ 720
0
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0
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969
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Comment: Comment: How can I get a taxid from an assembly id (e.g., GCA_003223415.1 -> 2026742)
2.0 years ago by O.rka ▴ 720
3
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2
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969
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How can I get a taxid from an assembly id (e.g., GCA_003223415.1 -> 2026742)
metagenomics accession ncbi taxonomy database
2.0 years ago by O.rka ▴ 720
3
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1
reply
647
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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 ★ 27k • written 2.0 years ago by ▴ 720
0
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1
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4.1k
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Comment: Comment: What are the recommended methods for merging de-novo assemblies?
2.0 years ago by O.rka ▴ 720
0
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0
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465
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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 ▴ 720
408 results • Page 2 of 9
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