Profile Posts Awards
Show
all questions tools blogs news tutorials forum answers comments
0
votes
1
reply
1.1k
views
How does MetaProdigal handle metagenomics where different genetic codes are used?
metagenomics metatranscriptomics binning
updated 3.3 years ago by ▴ 540 • written 3.3 years ago by ▴ 740
1
vote
2
replies
2.5k
views
Where to download a table of operons with genes for E. coli?
operon genes e coli transcription units
updated 3.3 years ago by ▴ 750 • written 8.3 years ago by ▴ 740
1
vote
1
reply
2.4k
views
Comment: Comment: How to compute module completion ratio of KEGG modules from KO identifiers? (com
3.3 years ago by O.rka ▴ 740
2
votes
3
replies
2.4k
views
How to compute module completion ratio of KEGG modules from KO identifiers? (command line)
database
updated 3.3 years ago by ▴ 540 • written 4.7 years ago by ▴ 740
0
votes
3
replies
1.0k
views
What is the best way to get all bacteria proteins from nr?
protists database nr
updated 3.4 years ago by 148k • written 3.4 years ago by ▴ 740
0
votes
0
replies
1.6k
views
Comment: Comment: Would you use HMMSCAN or HMMSEARCH when the query is much larger than the databa
3.4 years ago by O.rka ▴ 740
2
votes
2
replies
1.6k
views
Would you use HMMSCAN or HMMSEARCH when the query is much larger than the database?
nr hmmsearch hmmer hmm hmmscan
3.4 years ago by O.rka ▴ 740
1
vote
0
replies
7.3k
views
Comment: Comment: Is it possible to get taxonomy identifiers from diamond output without using --t
3.4 years ago by O.rka ▴ 740
0
votes
0
replies
605
views
Does anyone have any experience in hacking MaxBin2 to handle custom marker sets?
metagenomics maxbin2 binning
3.4 years ago by O.rka ▴ 740
1
vote
6
replies
1.5k
views
How to group transcripts by "gene" from different transcript assemblies?
assembly trinity rnaspades transcript
updated 3.4 years ago by ▴ 590 • written 3.4 years ago by ▴ 740
0
votes
0
replies
1.6k
views
Comment: Comment: How do you split metagenomic bins/MAGs into eukaryotic and prokaryotic?
3.4 years ago by O.rka ▴ 740
3
votes
3
replies
1.6k
views
How do you split metagenomic bins/MAGs into eukaryotic and prokaryotic?
protist metagenomics prokaryotic eukaryotic gtdbtk
updated 3.4 years ago by ★ 28k • written 3.4 years ago by ▴ 740
3
votes
1
reply
1.1k
views
Clarification on KEGG orthologs, why don't all have KEGG modules?
ortholog database kegg
updated 3.5 years ago by 3.8k • written 3.5 years ago by ▴ 740
0
votes
0
replies
810
views
Comment: Comment: What is the best short reader to very large reference fasta?
3.5 years ago by O.rka ▴ 740
0
votes
1
reply
810
views
Comment: Comment: What is the best short reader to very large reference fasta?
3.5 years ago by O.rka ▴ 740
1
vote
4
replies
810
views
What is the best short reader to very large reference fasta?
mapping alignment fastq bowtie2 bwa read
3.5 years ago by O.rka ▴ 740
1
vote
0
replies
721
views
Discussion on binning multiple metagenomes at the same time?
binning metagenomics mags
3.5 years ago by O.rka ▴ 740
0
votes
0
replies
571
views
How to use transcript coverage for ORF calls on contig?
gene-calling virus metatranscriptomics metagenomics
3.5 years ago by O.rka ▴ 740
0
votes
0
replies
2.4k
views
Comment: Comment: How to calculate differential methylation from nanopore reads?
3.6 years ago by O.rka ▴ 740
0
votes
0
replies
2.4k
views
Comment: Comment: How to calculate differential methylation from nanopore reads?
3.6 years ago by O.rka ▴ 740
1
vote
0
replies
15k
views
Answer: Answer: How to identify 16s sequences from binning data(contigs)?
3.6 years ago by O.rka ▴ 740
1
vote
4
replies
2.4k
views
How to calculate differential methylation from nanopore reads?
sequencing methylation
3.6 years ago by O.rka ▴ 740
0
votes
0
replies
1.6k
views
Comment: Comment: How to structure my edgeR model to incorporate a temporal variable and 2 categor
3.6 years ago by O.rka ▴ 740
0
votes
1
reply
1.6k
views
Comment: Comment: How to structure my edgeR model to incorporate a temporal variable and 2 categor
3.6 years ago by O.rka ▴ 740
5
votes
6
replies
1.6k
views
How to structure my edgeR model to incorporate a temporal variable and 2 categorical variables?
edgeR differential-gene-expression glm r
3.6 years ago by O.rka ▴ 740
0
votes
0
replies
1.6k
views
Comment: Comment: How to structure my edgeR model to incorporate a temporal variable and 2 categor
3.6 years ago by O.rka ▴ 740
1
vote
2
replies
1.7k
views
Understanding why `Design matrix not of full rank. The following coefficients not estimable` during GLM
edgeR design-matrix differential glm offtopic
updated 3.6 years ago by 88k • written 3.6 years ago by ▴ 740
5
votes
4
replies
11k
views
Why is `send` lower than `sstart` from blast format 6 output?
blast genomics
updated 3.7 years ago by • 0 • written 4.9 years ago by ▴ 740
0
votes
0
replies
662
views
How to calculate differential coverage between two groups?
differential bed bam rnaseq coverage
3.7 years ago by O.rka ▴ 740
0
votes
1
reply
1.1k
views
How to create a dummy GFF file from fasta?
fasta coverage bed gff
3.7 years ago by O.rka ▴ 740
0
votes
0
replies
1.1k
views
Answer: Answer: How to create a dummy GFF file from fasta?
3.7 years ago by O.rka ▴ 740
0
votes
1
reply
1.2k
views
What does the -0 flag of samtools fastq mean?
samtools
updated 3.7 years ago by ▴ 350 • written 3.7 years ago by ▴ 740
3
votes
1
reply
2.6k
views
Answer: C: Should I get my MS in Bioinformatics at UCSC or GA Tech
3.7 years ago by O.rka ▴ 740
0
votes
0
replies
1.7k
views
Comment: C: How to compute the "completeness" of a KEGG module using a set of KEGG orthologs
3.7 years ago by O.rka ▴ 740
0
votes
2
replies
1.7k
views
How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
kegg database metagenomics module
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 740
0
votes
0
replies
2.5k
views
Comment: C: How to get a mapping between KEGG module and KEGG orthologs?
3.7 years ago by O.rka ▴ 740
0
votes
0
replies
570
views
What do the + and - mean in KEGG Ortholog combinations under a particular Module?
kegg database module ortholog identifiers
3.7 years ago by O.rka ▴ 740
0
votes
0
replies
2.5k
views
Comment: C: How to get a mapping between KEGG module and KEGG orthologs?
3.7 years ago by O.rka ▴ 740
4
votes
3
replies
2.5k
views
How to get a mapping between KEGG module and KEGG orthologs?
KEGG Annotation Ortholog Module
updated 3.7 years ago by ▴ 270 • written 3.7 years ago by ▴ 740
0
votes
0
replies
719
views
Should "dispersion" in edgeR be calculated for entire dataset or just conditions being analyzed?
differential-gene-expression edgeR RNA-Seq
updated 10 months ago by 44k • written 3.8 years ago by ▴ 740
0
votes
1
reply
1.9k
views
Comment: C: How can I run "gene set enrichment" (not necessarily GSEA) with only one conditi
3.8 years ago by O.rka ▴ 740
2
votes
1
reply
3.9k
views
Answer: A: How to download a list of all KEGG orthologs with respect to KEGG module (or pat
3.8 years ago by O.rka ▴ 740
3
votes
3
replies
3.9k
views
How to download a list of all KEGG orthologs with respect to KEGG module (or pathway) in Python?
kegg database python
updated 2.4 years ago by • 0 • written 3.8 years ago by ▴ 740
0
votes
3
replies
1.9k
views
How can I run "gene set enrichment" (not necessarily GSEA) with only one condition?
metagenomics gene set enrichment analysis GSEA
3.8 years ago by O.rka ▴ 740
1
vote
0
replies
1.3k
views
What format are GTDB-Tk newick trees and how to extract specific node?
metagenomics gtdb database phylogeny
3.8 years ago by O.rka ▴ 740
0
votes
1
reply
1.0k
views
Why are there soo many hits when using KOFAMSCAN?
annotation protein metagenomics
updated 3.9 years ago by ★ 28k • written 3.9 years ago by ▴ 740
0
votes
0
replies
1.3k
views
Why is `scale-free topology` estimated as -sign(slope) * (R^2) in WGCNA?
WGCNA gene expression coexpression
3.9 years ago by O.rka ▴ 740
0
votes
0
replies
7.1k
views
Comment: C: WGCNA soft-threshold power selection
3.9 years ago by O.rka ▴ 740
0
votes
2
replies
3.5k
views
How to fix minimap2 -> samtools sort error (samtools sort: truncated file. Aborting)?
alignment
4.0 years ago by O.rka ▴ 740
0
votes
0
replies
987
views
Combining prodigal for metagenomics and transdecoder for metatranscriptomics in same dataset?
metagenomics metatranscriptomics orf calling
4.0 years ago by O.rka ▴ 740
410 results • Page 4 of 9
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6