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Comment: C: How to create vcf file with SNPs bed file and sorted bam file?
4.0 years ago by O.rka ▴ 740
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1.9k
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Comment: C: How to create vcf file with SNPs bed file and sorted bam file?
4.0 years ago by O.rka ▴ 740
1
vote
7
replies
1.9k
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How to create vcf file with SNPs bed file and sorted bam file?
RNA-Seq genome variant
updated 4.0 years ago by ▴ 180 • written 4.0 years ago by ▴ 740
0
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0
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1.9k
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Comment: C: How to create vcf file with SNPs bed file and sorted bam file?
4.0 years ago by O.rka ▴ 740
0
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0
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3.8k
views
Comment: C: metabat installation problem with conda
4.1 years ago by O.rka ▴ 740
0
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1
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841
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Can I use metatranscriptomic reads for coverage when doing metagenomic binning?
metagenomics metatranscriptomics binning
updated 4.1 years ago by ★ 28k • written 4.1 years ago by ▴ 740
1
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0
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3.8k
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Answer: A: EC number regular expression
4.1 years ago by O.rka ▴ 740
1
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1
reply
1.5k
views
How to look for enrichment of pathways using a list of EC numbers (enzyme)?
enzyme enrichment gsea picrust gene set
4.1 years ago by O.rka ▴ 740
6
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6
replies
7.3k
views
Is it possible to get taxonomy identifiers from diamond output without using --taxonmap during makedb?
diamond blast protein alignment taxonomy
updated 14 months ago by ▴ 30 • written 5.0 years ago by ▴ 740
0
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1
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1.9k
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What is an easy-to-use `conda` installable method for annotating proteins for eukaryotes?
annotation genome proteins eukaryotes
updated 4.3 years ago by ★ 28k • written 4.3 years ago by ▴ 740
0
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2
replies
1.8k
views
How to find all mapped locations of a read from PySam?
alignment
updated 4.4 years ago by 12k • written 4.4 years ago by ▴ 740
0
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0
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1.8k
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Comment: C: How to find all mapped locations of a read from PySam?
4.4 years ago by O.rka ▴ 740
0
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0
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846
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What does it mean when "-" or "+" join KEGG orthologs in a KEGG module definition?
kegg ortholog module annotation metagenomics
4.7 years ago by O.rka ▴ 740
0
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0
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2.5k
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Comment: C: Why is hmmsearch only using the 1st HMM in a concatenated HMM database?
4.7 years ago by O.rka ▴ 740
0
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1
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2.5k
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Comment: C: Why is hmmsearch only using the 1st HMM in a concatenated HMM database?
4.7 years ago by O.rka ▴ 740
2
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4
replies
2.5k
views
Why is hmmsearch only using the 1st HMM in a concatenated HMM database?
hmm hmmer protein domain bash script
updated 4.7 years ago by ★ 28k • written 4.7 years ago by ▴ 740
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1
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5.3k
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Comment: C: How to choose between --cut_ga, --cut_tc, and --cut_nc in hmmsearch? (hmmer)
4.7 years ago by O.rka ▴ 740
0
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1
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5.3k
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Comment: C: How to choose between --cut_ga, --cut_tc, and --cut_nc in hmmsearch? (hmmer)
4.7 years ago by O.rka ▴ 740
0
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1
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5.3k
views
Comment: C: How to choose between --cut_ga, --cut_tc, and --cut_nc in hmmsearch? (hmmer)
4.7 years ago by O.rka ▴ 740
4
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7
replies
5.3k
views
How to choose between --cut_ga, --cut_tc, and --cut_nc in hmmsearch? (hmmer)
alignment hmm protein domain
updated 4.7 years ago by ★ 28k • written 4.7 years ago by ▴ 740
0
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0
replies
612
views
How should I handle mapping to incomplete genome with many homologous regions?
RNA-Seq
updated 4.7 years ago by 20 • written 4.7 years ago by ▴ 740
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0
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1.2k
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Comment: C: How to get "best" taxon identifier from diamond output with staxids?
4.7 years ago by O.rka ▴ 740
0
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0
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3.7k
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Comment: C: BLAST multiple staxids
4.7 years ago by O.rka ▴ 740
0
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2
replies
1.2k
views
How to get "best" taxon identifier from diamond output with staxids?
metagenomics blast diamond alignment protein
4.7 years ago by O.rka ▴ 740
0
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1
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3.9k
views
Comment: C: How can I get taxonomy identifiers (staxids) using diamond? (Error: Invalid outp
4.7 years ago by O.rka ▴ 740
2
votes
3
replies
3.9k
views
How can I get taxonomy identifiers (staxids) using diamond? (Error: Invalid output format. Allowed values: 0,5,6,100,101,102)
alignment diamond
updated 4.7 years ago by 164k • written 4.7 years ago by ▴ 740
0
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0
replies
15k
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Comment: C: nr database Diamond
4.7 years ago by O.rka ▴ 740
0
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2
replies
1.6k
views
What are recommended parameters for removing rRNA from meta[transcript][gen]omics using bbduk.sh?
RNA-Seq metagenomics
4.7 years ago by O.rka ▴ 740
0
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0
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2.2k
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Comment: C: How can I transfer gene models to a new assembly?
4.7 years ago by O.rka ▴ 740
0
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0
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2.2k
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Comment: C: How can I transfer gene models to a new assembly?
4.7 years ago by O.rka ▴ 740
0
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0
replies
2.2k
views
Comment: C: How can I transfer gene models to a new assembly?
4.7 years ago by O.rka ▴ 740
2
votes
5
replies
815
views
If you generate a main text figure in a publication, does that deserve coauthorship?
academia
updated 4.8 years ago by ★ 28k • written 4.8 years ago by ▴ 740
0
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0
replies
7.3k
views
Comment: C: Is it possible to get taxonomy identifiers from diamond output without using --t
4.9 years ago by O.rka ▴ 740
0
votes
0
replies
11k
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Comment: C: Why is `send` lower than `sstart` from blast format 6 output?
4.9 years ago by O.rka ▴ 740
0
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0
replies
1.4k
views
Comment: C: Is there a tool for calculating the number of uniquely mapped reads, ambigiously
4.9 years ago by O.rka ▴ 740
0
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0
replies
1.4k
views
Comment: C: Is there a tool for calculating the number of uniquely mapped reads, ambigiously
4.9 years ago by O.rka ▴ 740
1
vote
5
replies
1.4k
views
Is there a tool for calculating the number of uniquely mapped reads, ambigiously mapped reads, and unmapped reads from sam/bam?
RNA-Seq
4.9 years ago by O.rka ▴ 740
0
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0
replies
48k
views
Comment: C: Fast download of FASTQ files from the European Nucleotide Archive (ENA)
4.9 years ago by O.rka ▴ 740
0
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1
reply
1.8k
views
Comment: C: Does fastq dump return interleaved files?
4.9 years ago by O.rka ▴ 740
0
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7
replies
1.8k
views
Does fastq dump return interleaved files?
sequence
updated 4.9 years ago by 86k • written 4.9 years ago by ▴ 740
0
votes
1
reply
2.6k
views
Basic fasterq-dump command is failing from `SIGNAL - Segmentation fault`
sequencing
updated 4.9 years ago by 86k • written 4.9 years ago by ▴ 740
5
votes
2
replies
2.4k
views
Remove duplicate reads before variant calling?
snp
updated 4.9 years ago by 20k • written 4.9 years ago by ▴ 740
0
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1
reply
2.0k
views
Comment: C: How do I know how much memory to use when piping to with BBMap suite (OutOfMemor
5.0 years ago by O.rka ▴ 740
4
votes
3
replies
2.0k
views
How do I know how much memory to use when piping to with BBMap suite (OutOfMemoryError)?
bbmap java memory reads
updated 13 months ago by 20k • written 5.0 years ago by ▴ 740
0
votes
0
replies
22k
views
Comment: C: What Does The Zero Mapping Quality Mean For The Bwa Mapper?
5.0 years ago by O.rka ▴ 740
2
votes
1
reply
1.0k
views
How to use ENCprime via coRdon with a custom background sequence set?
gene Bioconductor R
5.0 years ago by O.rka ▴ 740
1
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0
replies
1.0k
views
Answer: A: How to use ENCprime via coRdon with a custom background sequence set?
5.0 years ago by O.rka ▴ 740
2
votes
1
reply
951
views
Is there a method or HMM set to quickly determine if a sequence has a tRNA sequence for a large number of sequences/reads?
trna sequence
updated 5.0 years ago by ★ 28k • written 5.0 years ago by ▴ 740
0
votes
0
replies
805
views
Any alternatives to phylosift for identifying ribosomal proteins from metagenomic reads?
gene ribosomal
5.1 years ago by O.rka ▴ 740
0
votes
0
replies
1.5k
views
Comment: C: How to increase speed of BBMap's `reformat.sh` when randomly sampling reads?
5.1 years ago by O.rka ▴ 740
410 results • Page 5 of 9
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