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3
votes
3
replies
2.5k
views
How to fix "Please indicate the file directory in 'setting' file?" for MaxBin2?
maxbin2 binning metagenomics
updated 19 months ago by 44k • written 3.5 years ago by ▴ 740
0
votes
0
replies
927
views
Comment: Comment: t2t human reference genome for RNA-seq
21 months ago by O.rka ▴ 740
0
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2
replies
2.5k
views
Comment: Comment: How could I "recreate" UniRef50/UniRef90 with MMSEQS2?
21 months ago by O.rka ▴ 740
1
vote
4
replies
2.5k
views
How could I "recreate" UniRef50/UniRef90 with MMSEQS2?
clustering proteins annotation mmseqs2
updated 17 months ago by • 0 • written 21 months ago by ▴ 740
1
vote
2
replies
2.1k
views
Are there any tools that can create a very basic GTF file from contig sequences (no annotations really needed) ?
Assembly mapping
21 months ago by O.rka ▴ 740
0
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0
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2.1k
views
Answer: Answer: Are there any tools that can create a very basic GTF file from contig sequences
21 months ago by O.rka ▴ 740
0
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0
replies
463
views
What's the state-of-the-art for gene calling in eukaryotic transcriptomics?
modeling eukaryotic transcriptomics call gene
22 months ago by O.rka ▴ 740
0
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1
reply
1.4k
views
Comment: Comment: How can I run multiple sequence alignment for a large number of proteins (~10k)
23 months ago by O.rka ▴ 740
3
votes
5
replies
1.4k
views
How can I run multiple sequence alignment for a large number of proteins (~10k)
muscle msa protein multiple alignment sequence
updated 23 months ago by ★ 28k • written 23 months ago by ▴ 740
0
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0
replies
1.4k
views
Comment: Comment: How can I run multiple sequence alignment for a large number of proteins (~10k)
23 months ago by O.rka ▴ 740
0
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0
replies
1.7k
views
Comment: Comment: Any command line tools that can design primers from a multiple sequence alignmen
23 months ago by O.rka ▴ 740
0
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1
reply
1.7k
views
Comment: Comment: Any command line tools that can design primers from a multiple sequence alignmen
23 months ago by O.rka ▴ 740
0
votes
0
replies
756
views
Comment: Comment: What's best practice when determining a degenerate base when creating a primer?
23 months ago by O.rka ▴ 740
1
vote
2
replies
756
views
What's best practice when determining a degenerate base when creating a primer?
primer-design alignment genomics
23 months ago by O.rka ▴ 740
0
votes
1
reply
1.7k
views
Comment: Comment: Any command line tools that can design primers from a multiple sequence alignmen
23 months ago by O.rka ▴ 740
1
vote
6
replies
1.7k
views
Any command line tools that can design primers from a multiple sequence alignment?
primer-design genomics cli
23 months ago by O.rka ▴ 740
0
votes
1
reply
2.0k
views
Comment: Comment: What in silico PCR commandline tool do you use that can handle IUPAC characters?
24 months ago by O.rka ▴ 740
1
vote
1
reply
2.0k
views
Comment: Comment: What in silico PCR commandline tool do you use that can handle IUPAC characters?
24 months ago by O.rka ▴ 740
0
votes
0
replies
76k
views
Comment: Comment: Sequence length from Fasta
24 months ago by O.rka ▴ 740
9
votes
6
replies
2.0k
views
What in silico PCR commandline tool do you use that can handle IUPAC characters?
pcr amplicon primer
updated 8 months ago by 44k • written 24 months ago by ▴ 740
0
votes
0
replies
927
views
Comment: Comment: How to find full length ribosomal sequences for fungi?
24 months ago by O.rka ▴ 740
3
votes
3
replies
927
views
How to find full length ribosomal sequences for fungi?
ncbi ribosomal fungi nt
24 months ago by O.rka ▴ 740
0
votes
0
replies
392
views
How to estimate the memory requirements for Diamond given the database and query protein sizes?
alignment diamond memory requirements
24 months ago by O.rka ▴ 740
0
votes
0
replies
854
views
Comment: Comment: How to "enrich" a large set of proteins (>11M) for protein hits in UniRef90?
24 months ago by O.rka ▴ 740
0
votes
1
reply
854
views
Comment: Comment: How to "enrich" a large set of proteins (>11M) for protein hits in UniRef90?
24 months ago by O.rka ▴ 740
0
votes
4
replies
854
views
How to "enrich" a large set of proteins (>11M) for protein hits in UniRef90?
uniref proteins alignment
24 months ago by O.rka ▴ 740
0
votes
0
replies
1.6k
views
Comment: Comment: How to extract unmapped reads if you have paired end reads (fastq) and mapped BA
2.1 years ago by O.rka ▴ 740
0
votes
1
reply
1.6k
views
Comment: Comment: How to extract unmapped reads if you have paired end reads (fastq) and mapped BA
2.1 years ago by O.rka ▴ 740
3
votes
4
replies
1.6k
views
How to extract unmapped reads if you have paired end reads (fastq) and mapped BAM file?
fastq bam sam reads
2.1 years ago by O.rka ▴ 740
2
votes
2
replies
1.2k
views
What's the benefit of using the `no_alt_analysis_set` Bowtie2 index over the primary assembly?
human rnaseq mapping metagenomics
updated 2.2 years ago by 86k • written 2.2 years ago by ▴ 740
0
votes
1
reply
753
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 2.3 years ago by 148k • written 2.3 years ago by ▴ 740
0
votes
0
replies
2.1k
views
Comment: Comment: Are there any tools that automatically detect where to truncate forward and reve
2.3 years ago by O.rka ▴ 740
0
votes
0
replies
666
views
Comment: Comment: How to calculate position-specific fastq stats?
2.3 years ago by O.rka ▴ 740
0
votes
2
replies
666
views
How to calculate position-specific fastq stats?
rnaseq fastq metagenomics genomics
2.3 years ago by O.rka ▴ 740
0
votes
3
replies
2.1k
views
Are there any tools that automatically detect where to truncate forward and reverse reads for 16S (DADA2)?
16s dada2 illumina metagenomics qiime2
2.3 years ago by O.rka ▴ 740
0
votes
1
reply
1.4k
views
Comment: Comment: Is it required for all sequences to be same length when clustering OTUs in metag
2.4 years ago by O.rka ▴ 740
1
vote
3
replies
1.4k
views
Is it required for all sequences to be same length when clustering OTUs in metagenomics (ONT Nanopore)
otu metagenomics clustering nanopore
updated 2.4 years ago by 3.2k • written 2.4 years ago by ▴ 740
0
votes
0
replies
776
views
Comment: Comment: What percent identity is recommended for detecting protein homology within a spe
2.4 years ago by O.rka ▴ 740
0
votes
2
replies
776
views
What percent identity is recommended for detecting protein homology within a species?
alignment genomics proteomics
2.4 years ago by O.rka ▴ 740
0
votes
0
replies
2.2k
views
Comment: Comment: Is there a tool that calculates genome coverage? (e.g., 1X, 10X, 100X)
2.4 years ago by O.rka ▴ 740
0
votes
1
reply
2.2k
views
Comment: Comment: Is there a tool that calculates genome coverage? (e.g., 1X, 10X, 100X)
2.4 years ago by O.rka ▴ 740
0
votes
1
reply
2.2k
views
Comment: Comment: Is there a tool that calculates genome coverage? (e.g., 1X, 10X, 100X)
2.4 years ago by O.rka ▴ 740
1
vote
6
replies
2.2k
views
Is there a tool that calculates genome coverage? (e.g., 1X, 10X, 100X)
ncbi metagenomics submission
2.4 years ago by O.rka ▴ 740
0
votes
1
reply
571
views
Software to produce position-specific conservation of multiple sequence alignment results?
transcriptomics genomics alignment proteomics
updated 2.4 years ago by ★ 28k • written 2.4 years ago by ▴ 740
0
votes
1
reply
1.2k
views
How to count the number of multimapped reads from a bam file?
rnaseq mapping bowtie2 featurecounts
updated 2.5 years ago by ★ 1.6k • written 2.5 years ago by ▴ 740
1
vote
1
reply
1.0k
views
Advice on mapping reads to polyploid de-novo assembly
assembly RNA-Seq
updated 2.5 years ago by 7.0k • written 4.9 years ago by ▴ 740
0
votes
1
reply
688
views
How do you predict regions on a protein that are exposed on the cell surface?
protein antibody hmm domain
updated 2.5 years ago by ★ 28k • written 2.5 years ago by ▴ 740
0
votes
0
replies
1.3k
views
Comment: Comment: How can I get a taxid from an assembly id (e.g., GCA_003223415.1 -> 2026742)
2.6 years ago by O.rka ▴ 740
3
votes
2
replies
1.3k
views
How can I get a taxid from an assembly id (e.g., GCA_003223415.1 -> 2026742)
metagenomics accession ncbi taxonomy database
2.6 years ago by O.rka ▴ 740
3
votes
1
reply
842
views
What are the suggested parameters for running IQ-TREE on a protein alignment for phylogeny?
protein metagenomics phylogeny iqtree
updated 2.6 years ago by ★ 28k • written 2.6 years ago by ▴ 740
410 results • Page 2 of 9
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