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4
replies
1.7k
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How can I use bedtools complement, sam mapping file, and my gtf file to get number of reads for intergenic regions?
RNA-Seq
6.4 years ago by O.rka ▴ 750
0
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0
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17k
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Comment: C: Easiest way to compute RNA-Seq mapping stats (exons, introns, intergenic)?
6.4 years ago by O.rka ▴ 750
3
votes
2
replies
4.2k
views
How to use BBMap's reformat.sh to correctly interleaved reads?
genome mapping next-gen fastq
updated 6.5 years ago by 35k • written 6.5 years ago by ▴ 750
1
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0
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4.2k
views
Answer: A: How to use BBMap's reformat.sh to correctly interleaved reads?
6.5 years ago by O.rka ▴ 750
1
vote
0
replies
1.5k
views
Which automatic metagenome binning tools can handle viral bins?
assembly metagenomics binning
6.5 years ago by O.rka ▴ 750
0
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0
replies
5.1k
views
Comment: C: How to calculate percent identity from sam file?
6.5 years ago by O.rka ▴ 750
0
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1
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5.1k
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Comment: C: How to calculate percent identity from sam file?
6.5 years ago by O.rka ▴ 750
0
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1
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5.1k
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Comment: C: How to calculate percent identity from sam file?
6.5 years ago by O.rka ▴ 750
0
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0
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5.1k
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Comment: C: How to calculate percent identity from sam file?
6.5 years ago by O.rka ▴ 750
0
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0
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5.1k
views
Comment: C: How to calculate percent identity from sam file?
6.5 years ago by O.rka ▴ 750
3
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11
replies
5.1k
views
How to calculate percent identity from sam file?
mapping assembly sam samtools cigar
6.5 years ago by O.rka ▴ 750
1
vote
1
reply
1.6k
views
Is there a tool that filters a sam/bam file by the following: (1) similarity score; (2) length fraction?
RNA-Seq alignment sequencing next-gen
6.5 years ago by O.rka ▴ 750
0
votes
0
replies
687
views
Is there a tool that can identify frame shifted proteins from an assembly?
software error RNA-Seq genome
6.5 years ago by O.rka ▴ 750
13
votes
10
replies
5.6k
views
Is there any benefit in sorting a sam/bam file by coordinates vs. queryname?
alignment
updated 6.5 years ago by 35k • written 6.5 years ago by ▴ 750
0
votes
0
replies
916
views
How to get GO terms from EcoCyc gene identifiers?
genome e coli ecocyc gene ontology
6.6 years ago by O.rka ▴ 750
0
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0
replies
6.0k
views
Comment: C: How to repair a gff/gtf file that is missing gene id, gene name, and transcript
6.7 years ago by O.rka ▴ 750
1
vote
2
replies
6.0k
views
How to repair a gff/gtf file that is missing gene id, gene name, and transcript name?
annotation alignment RNA-Seq gene gtf
6.7 years ago by O.rka ▴ 750
0
votes
0
replies
3.8k
views
Comment: C: How to map RNA-seq with hisat2, stringtie, an assembly fasta, a gtf file, and a
6.7 years ago by O.rka ▴ 750
2
votes
2
replies
3.8k
views
How to map RNA-seq with hisat2, stringtie, an assembly fasta, a gtf file, and a transcript fasta?
hisat2 mapping transcriptome stringtie
updated 6.7 years ago by 15k • written 6.7 years ago by ▴ 750
0
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0
replies
4.3k
views
Answer: A: Which Ensembl chromosome sequence file is used for the gff3 files?
6.8 years ago by O.rka ▴ 750
4
votes
7
replies
4.3k
views
Which Ensembl chromosome sequence file is used for the gff3 files?
ensembl gff3 genome chromosome human
6.8 years ago by O.rka ▴ 750
1
vote
5
replies
2.8k
views
How to download all premRNA sequences (exons + introns) for human GRCh38 with Ensembl IDs?
RNA-Seq database ensembl human sequences
updated 6.8 years ago by 20 • written 6.8 years ago by ▴ 750
0
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1
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4.3k
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Comment: C: Which Ensembl chromosome sequence file is used for the gff3 files?
6.8 years ago by O.rka ▴ 750
0
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1
reply
4.3k
views
Comment: C: Which Ensembl chromosome sequence file is used for the gff3 files?
6.8 years ago by O.rka ▴ 750
0
votes
0
replies
2.8k
views
Comment: C: How to download all premRNA sequences (exons + introns) for human GRCh38 with En
6.8 years ago by O.rka ▴ 750
0
votes
1
reply
3.5k
views
Does MetaCyc or BioCyc have an equivalent of KEGG orthologs that could be blasted against locally?
metacyc biocyc humann2 orthologs metagenomics
updated 6.8 years ago by ▴ 30 • written 6.8 years ago by ▴ 750
7
votes
5
replies
4.2k
views
How to merge quality trimmed interlaced reads?
RNA-Seq
updated 6.8 years ago by 20 • written 7.5 years ago by ▴ 750
0
votes
0
replies
3.8k
views
Comment: C: Where can I download ALL pfam flat-file annotations?
6.8 years ago by O.rka ▴ 750
0
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1
reply
3.8k
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Comment: C: Where can I download ALL pfam flat-file annotations?
6.8 years ago by O.rka ▴ 750
1
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0
replies
3.3k
views
Comment: C: In GSEA, how can one "correlate" gene expression with categorical phenotype data
6.8 years ago by O.rka ▴ 750
0
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1
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3.3k
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Comment: C: In GSEA, how can one "correlate" gene expression with categorical phenotype data
6.8 years ago by O.rka ▴ 750
5
votes
4
replies
3.3k
views
In GSEA, how can one "correlate" gene expression with categorical phenotype data?
gsea correlation pearson genes expression
updated 6.8 years ago by 89k • written 6.8 years ago by ▴ 750
0
votes
1
reply
4.4k
views
Run GSEA with custom gene sets?
gsea custom gene enrichment differential-abundance
updated 6.8 years ago by 35k • written 6.8 years ago by ▴ 750
17
votes
9
replies
23k
views
6 follow
How to download genome assemblies from NCBI with a list of GCA identifiers?
ncbi Assembly
updated 2.5 years ago by 45k • written 6.9 years ago by ▴ 750
0
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1
reply
7.4k
views
Comment: C: How to use Biopython for fetching metadata of NCBI/GenBank/RefSeq assembly ident
6.9 years ago by O.rka ▴ 750
0
votes
0
replies
7.4k
views
Comment: C: How to use Biopython for fetching metadata of NCBI/GenBank/RefSeq assembly ident
6.9 years ago by O.rka ▴ 750
14
votes
4
replies
7.4k
views
How to use Biopython for fetching metadata of NCBI/GenBank/RefSeq assembly identifiers?
biopython ncbi entrez Assembly fetch
updated 6.9 years ago by 3.4k • written 6.9 years ago by ▴ 750
0
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0
replies
7.4k
views
Comment: C: Why is Neighbor Joining method better than UPGMA for phylogenetic tree reconstru
6.9 years ago by O.rka ▴ 750
0
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1
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7.4k
views
Comment: C: Why is Neighbor Joining method better than UPGMA for phylogenetic tree reconstru
6.9 years ago by O.rka ▴ 750
3
votes
4
replies
7.4k
views
Why is Neighbor Joining method better than UPGMA for phylogenetic tree reconstruction from protein sequences?
Assembly alignment phylogenetics upgma
6.9 years ago by O.rka ▴ 750
0
votes
2
replies
23k
views
Comment: C: How to download genome assemblies from NCBI with a list of GCA identifiers?
6.9 years ago by O.rka ▴ 750
0
votes
1
reply
3.0k
views
How to ignore truncation error with PySam?
pysam sam alignment mapping python
updated 6.9 years ago by 20 • written 6.9 years ago by ▴ 750
0
votes
1
reply
6.1k
views
Comment: C: What are the recommended methods for merging de-novo assemblies?
6.9 years ago by O.rka ▴ 750
0
votes
2
replies
6.1k
views
Comment: C: What are the recommended methods for merging de-novo assemblies?
6.9 years ago by O.rka ▴ 750
0
votes
1
reply
6.1k
views
Comment: C: What are the recommended methods for merging de-novo assemblies?
6.9 years ago by O.rka ▴ 750
6
votes
18
replies
6.1k
views
6 follow
What are the recommended methods for merging de-novo assemblies?
Assembly sequencing
updated 3.4 years ago by ▴ 1000 • written 6.9 years ago by ▴ 750
0
votes
1
reply
6.1k
views
Comment: C: What are the recommended methods for merging de-novo assemblies?
6.9 years ago by O.rka ▴ 750
0
votes
2
replies
6.1k
views
Comment: C: What are the recommended methods for merging de-novo assemblies?
6.9 years ago by O.rka ▴ 750
0
votes
0
replies
2.5k
views
Comment: C: How to extract reads that match k-mer profiles from a collection of sequences?
6.9 years ago by O.rka ▴ 750
0
votes
0
replies
2.4k
views
Comment: C: Extracted mapped shotgun metagenomic reads to reference genome. SPAdes or metaSP
6.9 years ago by O.rka ▴ 750
410 results • Page 7 of 9
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