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1
vote
2
replies
1.4k
views
Statistically defining deep branching clades in phylogenetic tree
phylogenetics trees
5.7 years ago by Daniel ★ 4.0k
20
votes
10
replies
11k
views
Looking For A Command Line Version Of Ncbi Taxonomy 'Stratification' Tool
taxonomy blast pipeline ncbi
updated 10 months ago by 43k • written 12.3 years ago by ★ 4.0k
4
votes
3
replies
2.5k
views
Error passing generated fasta to blastn in biopython
biopython blast blastn
updated 6.4 years ago by 20 • written 7.6 years ago by ★ 4.0k
8
votes
5
replies
12k
views
What is the limiting factor for trimmomatic speed and how can it be increased?
trimmomatic fastq
7.1 years ago by Daniel ★ 4.0k
5
votes
2
replies
4.9k
views
Using pysam to parse bamfile and fetch based on bedfile, looking to speed up code.
python pysam
7.7 years ago by Daniel ★ 4.0k
4
votes
2
replies
5.5k
views
Otu Percentage Identity Related To Taxon Level
taxonomy
updated 7.9 years ago by • 0 • written 11.1 years ago by ★ 4.0k
1
vote
2
replies
1.7k
views
Best way to determine gene positions in a related strain, from a well annotated reference? (and plus some RNAseq?)
maker anotation
updated 7.9 years ago by ▴ 80 • written 7.9 years ago by ★ 4.0k
3
votes
17
replies
8.1k
views
join non-overlapping paired-end reads
paired-end illumina
updated 2.0 years ago by 43k • written 9.9 years ago by ★ 4.0k
2
votes
3
replies
1.3k
views
Can a lack of exome coverage disproportionately call snRNAs as significantly changing (and hide standard genes)?
RNA-Seq snRNA
updated 8.1 years ago by 7.3k • written 8.1 years ago by ★ 4.0k
0
votes
6
replies
2.9k
views
RNAseq comparisons (tophat->HTSeq->edgeR) return only a few sig diffs, and all snRNA. Pos. bias? Further options?
RNA-Seq HTSeq snRNA
8.2 years ago by Daniel ★ 4.0k
17
votes
4
replies
13k
views
Rdp, Greengenes And Arb-Silva. Are There Any Advantages Of One Over The Other?
updated 8.2 years ago by 11k • written 13.1 years ago by ★ 4.0k
0
votes
0
replies
1.5k
views
For transposon mapping, how important is sequence length? Is Illumina 75x2 PE sufficient versus the 150x2 expense?
NGS transposons
updated 20 months ago by 43k • written 8.4 years ago by ★ 4.0k
0
votes
2
replies
4.0k
views
Is there a command line protocol for looking doing ontology/pathway analysis (i.e. not through DAVID or PANTHER)? How do the Pros do it?
RNA-Seq ontology protocol
updated 19 months ago by 43k • written 8.6 years ago by ★ 4.0k
5
votes
2
replies
2.3k
views
IGB is consistently crashing and I can't understand why
IGB software
updated 19 months ago by 43k • written 8.7 years ago by ★ 4.0k
6
votes
4
replies
4.6k
views
Looking for a tool for finding 'nearest feature' given genomic coordinates?
ChIP-Seq genome
updated 18 months ago by 43k • written 8.7 years ago by ★ 4.0k
5
votes
3
replies
3.2k
views
Determining Transcription Start Sites from multiple RNAseq bioreps
TSS-prediction RNA-Seq
updated 18 months ago by 43k • written 8.7 years ago by ★ 4.0k
19
votes
28
replies
15k
views
8 follow
Subsample BAM to fixed number of alignments
subsampling bam
updated 16 months ago by 43k • written 8.9 years ago by ★ 4.0k
2
votes
5
replies
2.3k
views
Mapping low coverage RNAseq at gene-level rather than exon level
RNA-Seq
updated 15 months ago by 43k • written 8.9 years ago by ★ 4.0k
2
votes
6
replies
2.3k
views
Is there a more optimal SAM orientation parsing method?
perl SAM
updated 14 months ago by 43k • written 9.0 years ago by ★ 4.0k
4
votes
2
replies
4.1k
views
Using Bioperl To Match Primer Sites. Difficulty With Iupac.Pm
bioperl
updated 3.1 years ago by 43k • written 11.3 years ago by ★ 4.0k
6
votes
13
replies
3.2k
views
Error when fuzzy sequence matching using String::Approx in perl
fuzzy-matching perl
updated 2.5 years ago by 43k • written 9.8 years ago by ★ 4.0k
4
votes
10
replies
2.7k
views
Every one of my illumina seqs have an 'N' at base 18 and 48, and -14 on the reverse. I don't think this is normal... Anyone seen this before?
illumina
updated 2.4 years ago by 43k • written 9.9 years ago by ★ 4.0k
1
vote
1
reply
2.2k
views
Is there a succinct method of isolating sequences phylogenetically similar to a distinct reference clade.
alignment amplicon blast
updated 2.6 years ago by 43k • written 9.9 years ago by ★ 4.0k
1
vote
1
reply
2.5k
views
Correcting sequence reads based on ORF disruption from reference sequence.
error-correction alignment next-gen
updated 2.5 years ago by 43k • written 9.9 years ago by ★ 4.0k
0
votes
1
reply
4.9k
views
Attempting To Utilise The New Entrez Direct Package But Having Difficulty With Pubmed And Nucleotide Xml Parsing
entrez eutils xml parsing
updated 10.1 years ago by 49k • written 10.1 years ago by ★ 4.0k
1
vote
7
replies
3.8k
views
Error When Reading Tigr Format Xml With Bioperl
bioperl xml
updated 10.5 years ago by 100k • written 10.5 years ago by ★ 4.0k
10
votes
6
replies
4.1k
views
Assess The Characteristics Of High Numbers Of Bacterial Species
10.8 years ago by Daniel ★ 4.0k
10
votes
9
replies
8.0k
views
Parsing Genbank Format In Bioperl.
bioperl genbank
updated 11.3 years ago by 5.0k • written 11.3 years ago by ★ 4.0k
0
votes
4
replies
2.8k
views
Is There A Library Of Fosmid Sequences?
sequence
updated 12.5 years ago by 16k • written 12.5 years ago by ★ 4.0k
8
votes
8
replies
3.8k
views
Stand Alone Otu Generation Program (Ngs)
software
updated 13.1 years ago by ★ 1.1k • written 13.1 years ago by ★ 4.0k
4
votes
11
replies
2.9k
views
Experiences With Pangea
pipeline
13.3 years ago by Daniel ★ 4.0k
31 results • Page 1 of 1
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