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2
votes
5
replies
2.7k
views
primer design to discriminate sequences in intron-exon MSA
primer MSA intron-exon
updated 5 weeks ago by • 0 • written 6.7 years ago by ▴ 630
16
votes
7
replies
6.2k
views
6 follow
rRNA decontamination of RNA-Seq reads (tool choice, introns etc)
rRNA intron RNA-Seq bbsuite sormeRNA
updated 15 months ago by 142k • written 4.5 years ago by ▴ 630
0
votes
0
replies
340
views
off-target predictions to prioritize list of sgRNA designs
sgRNA CRISPR CHOPCHOP
2.1 years ago by Anand Rao ▴ 630
6
votes
5
replies
2.4k
views
PDB file pairwise alignment software choice
structure pairwise parsing alignment classification
updated 2.3 years ago by ▴ 10 • written 2.5 years ago by ▴ 630
6
votes
6
replies
3.2k
views
bbduk flags 'tossbrokenreads' and 'nullifybrokenquality'
BBMap BBduk flags
updated 2.5 years ago by ▴ 30 • written 4.6 years ago by ▴ 630
0
votes
4
replies
1.2k
views
FASTQ headers need additional info?
format FASTQ
2.8 years ago by Anand Rao ▴ 630
1
vote
3
replies
1.1k
views
Testing independence between 5' and 3' terminal sequences in a DNA database
sequence cluster DNA independence testing
updated 3.1 years ago by 100k • written 3.1 years ago by ▴ 630
0
votes
2
replies
770
views
Identification of protein domain encoding multi-exon genomic intervals
geneprediction
3.1 years ago by Anand Rao ▴ 630
0
votes
0
replies
765
views
Identifying truncated protein domain encoding DNA sequences
protein domain truncation AUGUSTUS fastBlockSearch
3.6 years ago by Anand Rao ▴ 630
11
votes
8
replies
2.7k
views
SizeFactors for BAM normalization
deepTools bamCoverage sizeFactors DESeq2
updated 3.8 years ago by 104k • written 3.8 years ago by ▴ 630
3
votes
4
replies
1.2k
views
Standardizing 3rd party GFF3 file
GFF3 format validation
3.8 years ago by Anand Rao ▴ 630
13
votes
11
replies
3.4k
views
interpreting GC-bias compute and correct results from DeepTools
GC-bias deepTools
3.9 years ago by Anand Rao ▴ 630
4
votes
7
replies
2.3k
views
Fixing BAM file errors reported by Picard ValidateSamFile, and in featureCounts' outfile
BAM featureCounts Picard ValidateSamFile
3.9 years ago by Anand Rao ▴ 630
2
votes
5
replies
975
views
What is acceptable contaminant levels for RNA-Seq mapping?
RNA-Seq decontamination
4.0 years ago by Anand Rao ▴ 630
0
votes
0
replies
758
views
Tools for mRNA-Seq time series DGE GCN and other analyses
time-course RNA-Seq time-series
updated 11 months ago by 43k • written 4.0 years ago by ▴ 630
0
votes
3
replies
1.0k
views
fastq file sub-sampling during per position quality score graphing
FASTX_Toolkit FastQC
4.0 years ago by Anand Rao ▴ 630
0
votes
5
replies
4.7k
views
7 follow
map gene gain loss on species tree
gene-tree tree reconciliation species
updated 18 months ago by ▴ 430 • written 8.6 years ago by ▴ 630
6
votes
10
replies
1.9k
views
BBmap pipeline output varies across replicated runs
bbmap reproducibility clumpify
4.6 years ago by Anand Rao ▴ 630
10
votes
8
replies
3.6k
views
STAR aligner maps 0 reads to multiple loci, but 3.7% to too many loci - meaning?
STAR RNA-Seq mapping
updated 4.6 years ago by 35k • written 4.6 years ago by ▴ 630
2
votes
2
replies
787
views
List of plant long read genome assemblies
plant genome long read Assembly
4.7 years ago by Anand Rao ▴ 630
1
vote
2
replies
1.4k
views
Multiple sequence alignment statistics
MSA statistics
updated 4.9 years ago by 20 • written 5.0 years ago by ▴ 630
1
vote
3
replies
2.6k
views
Using row order of one heatmap for a new heatmap
Heatmap R row reorder plot
4.9 years ago by Anand Rao ▴ 630
1
vote
8
replies
1.2k
views
How can I perform pairwise comparison of protein secondary structure?
secondary structure protein structure alignment
updated 4.9 years ago by ★ 27k • written 4.9 years ago by ▴ 630
3
votes
1
reply
1.3k
views
Evaluating protein structure predictions
protein structure evaluation ProQ QMEAN
updated 4.9 years ago by ▴ 390 • written 4.9 years ago by ▴ 630
0
votes
1
reply
1.1k
views
RepeatModeler contig size filter and parallelization
RepeatModeler Contig length Parallel
5.1 years ago by Anand Rao ▴ 630
0
votes
0
replies
1.6k
views
RepeatModeler run error troubleshooting
RepeatModeler RepeatMasker BuildDatabase blastdb
5.2 years ago by Anand Rao ▴ 630
0
votes
0
replies
1.4k
views
Extract VCF from genome assemblies of multiple individuals
SNP Structural Variation VCF Genomes alignment
5.2 years ago by Anand Rao ▴ 630
2
votes
6
replies
1.5k
views
Which NGS aligner to find inexact matches
DNA alignment NGS aligner genome coordinates NGS
5.3 years ago by Anand Rao ▴ 630
4
votes
4
replies
2.4k
views
bedtools subtract still overlaps by 1bp?
bedtools getfasta slop subtract
updated 5.3 years ago by 16k • written 5.3 years ago by ▴ 630
1
vote
1
reply
3.1k
views
Choosing tool for DNA secondary structure stem-loop prediction
secondary stem loop DNA software
5.3 years ago by Anand Rao ▴ 630
20
votes
4
replies
9.5k
views
Bulk download of entire BioProject SRA
SRA NCBI sratoolkit entrez utilities BioProject
updated 5.3 years ago by 3.2k • written 5.3 years ago by ▴ 630
12
votes
2
replies
3.7k
views
Visualize multiple GFF files
GFF overlap statistics visualization
updated 5.4 years ago by 21k • written 5.8 years ago by ▴ 630
4
votes
2
replies
4.5k
views
mummerplot for genome self alignment NOT yielding full length diagonal graph
mummer nucmer mummerplot genome alignment
5.4 years ago by Anand Rao ▴ 630
3
votes
5
replies
2.1k
views
CD-HIT results without sorting by length
clustering CD-HIT sort length
5.4 years ago by Anand Rao ▴ 630
2
votes
5
replies
1.5k
views
Merge intervals between but NOT within 2 BED files
bedtools merge overlap bedops
updated 5.7 years ago by 35k • written 5.7 years ago by ▴ 630
1
vote
3
replies
1.6k
views
bedtools strategy to report both merged AND unmerged intervals
bedtools merge unmerged gff3
5.8 years ago by Anand Rao ▴ 630
0
votes
0
replies
1.4k
views
AUGUSTUS protein profile run error
augustus ppx error
5.8 years ago by Anand Rao ▴ 630
2
votes
2
replies
1.0k
views
collapsing GFF coordinates with common start OR stop
GFF parse script bedtools Perl
updated 5.8 years ago by 35k • written 5.8 years ago by ▴ 630
8
votes
4
replies
4.7k
views
SPAdes assembler k-mer > default 127 possible?
Genome assembly SPAdes k-mer
updated 6.0 years ago by ▴ 50 • written 6.7 years ago by ▴ 630
11
votes
10
replies
5.8k
views
Best mapping software to generate BAM file
BAM mapping
updated 6.5 years ago by 20 • written 6.6 years ago by ▴ 630
0
votes
0
replies
1.5k
views
Simulating Core / Accessory genome for incomplete genome assemblies
Core Accessory Simulation Incomplete draft
6.6 years ago by Anand Rao ▴ 630
3
votes
3
replies
2.5k
views
Assess and correct any GC bias in Illumina HiSeq 4000 data
GC bias Illumina HiSeq 4000 coverage depth
updated 6.6 years ago by 20k • written 6.6 years ago by ▴ 630
9
votes
3
replies
7.7k
views
Illumina R1 vs. R2 read quality differences - reasons?
read quality illumina PE
updated 6.6 years ago by 100k • written 6.6 years ago by ▴ 630
0
votes
0
replies
1.5k
views
ALLPATHS-LG error correction Perl script run error
ALLPATHS-LG error correction Perl run error
updated 6.6 years ago by 20 • written 6.7 years ago by ▴ 630
7
votes
4
replies
4.4k
views
How to measure NGS depth coverage bias
NGS Illumina sequencing depth coverage bias
updated 6.6 years ago by ★ 1.6k • written 6.6 years ago by ▴ 630
1
vote
1
reply
2.2k
views
REAPR run error
REAPR SMALT run error
6.7 years ago by Anand Rao ▴ 630
0
votes
1
reply
1.6k
views
a5miseq syntax help
a5miseq syntax Fastq format custom adapters
updated 6.7 years ago by 142k • written 6.7 years ago by ▴ 630
1
vote
0
replies
2.5k
views
A5 pipeline begin and end
A5 pipeline genome assembly assembler
6.7 years ago by Anand Rao ▴ 630
0
votes
2
replies
1.3k
views
a5pipeline.pl run error
a5_pipeline.pl run error phred encoding
6.7 years ago by Anand Rao ▴ 630
0
votes
0
replies
1.3k
views
Aligning gene sequences
Splice-aware Gene alignment Exon-Intron boundary
6.7 years ago by Anand Rao ▴ 630
79 results • Page 1 of 2
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