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questions
2
votes
5
replies
3.2k
views
primer design to discriminate sequences in intron-exon MSA
primer
MSA
intron-exon
updated 10 months ago by
Amruta
• 0 • written 7.4 years ago by
Anand Rao
▴ 640
16
votes
7
replies
7.3k
views
6 follow
rRNA decontamination of RNA-Seq reads (tool choice, introns etc)
rRNA
intron
RNA-Seq
bbsuite
sormeRNA
updated 2.0 years ago by
GenoMax
149k • written 5.2 years ago by
Anand Rao
▴ 640
0
votes
0
replies
458
views
off-target predictions to prioritize list of sgRNA designs
sgRNA
CRISPR
CHOPCHOP
2.9 years ago by
Anand Rao
▴ 640
6
votes
5
replies
3.0k
views
PDB file pairwise alignment software choice
structure
pairwise
parsing
alignment
classification
updated 3.0 years ago by
berkyalcinkaya55
▴ 10 • written 3.3 years ago by
Anand Rao
▴ 640
6
votes
6
replies
3.8k
views
bbduk flags 'tossbrokenreads' and 'nullifybrokenquality'
BBMap
BBduk
flags
updated 3.3 years ago by
Juan MONROY-NIETO
▴ 30 • written 5.3 years ago by
Anand Rao
▴ 640
0
votes
4
replies
1.5k
views
FASTQ headers need additional info?
format
FASTQ
3.6 years ago by
Anand Rao
▴ 640
1
vote
3
replies
1.3k
views
Testing independence between 5' and 3' terminal sequences in a DNA database
sequence
cluster
DNA
independence
testing
updated 3.9 years ago by
Istvan Albert
102k • written 3.9 years ago by
Anand Rao
▴ 640
0
votes
2
replies
900
views
Identification of protein domain encoding multi-exon genomic intervals
geneprediction
3.9 years ago by
Anand Rao
▴ 640
0
votes
0
replies
892
views
Identifying truncated protein domain encoding DNA sequences
protein domain
truncation
AUGUSTUS
fastBlockSearch
4.4 years ago by
Anand Rao
▴ 640
12
votes
8
replies
3.4k
views
SizeFactors for BAM normalization
deepTools
bamCoverage
sizeFactors
DESeq2
updated 4.5 years ago by
Devon Ryan
105k • written 4.5 years ago by
Anand Rao
▴ 640
3
votes
4
replies
1.5k
views
Standardizing 3rd party GFF3 file
GFF3
format
validation
4.6 years ago by
Anand Rao
▴ 640
13
votes
11
replies
4.2k
views
interpreting GC-bias compute and correct results from DeepTools
GC-bias
deepTools
4.6 years ago by
Anand Rao
▴ 640
4
votes
7
replies
2.9k
views
Fixing BAM file errors reported by Picard ValidateSamFile, and in featureCounts' outfile
BAM
featureCounts
Picard
ValidateSamFile
4.7 years ago by
Anand Rao
▴ 640
2
votes
5
replies
1.2k
views
What is acceptable contaminant levels for RNA-Seq mapping?
RNA-Seq
decontamination
4.8 years ago by
Anand Rao
▴ 640
0
votes
0
replies
880
views
Tools for mRNA-Seq time series DGE GCN and other analyses
time-course
RNA-Seq
time-series
updated 20 months ago by
Ram
44k • written 4.8 years ago by
Anand Rao
▴ 640
0
votes
3
replies
1.2k
views
fastq file sub-sampling during per position quality score graphing
FASTX_Toolkit
FastQC
4.8 years ago by
Anand Rao
▴ 640
0
votes
5
replies
5.2k
views
7 follow
map gene gain loss on species tree
gene-tree
tree
reconciliation
species
updated 2.3 years ago by
Ric
▴ 440 • written 9.4 years ago by
Anand Rao
▴ 640
6
votes
10
replies
2.3k
views
BBmap pipeline output varies across replicated runs
bbmap
reproducibility
clumpify
5.3 years ago by
Anand Rao
▴ 640
10
votes
8
replies
4.2k
views
STAR aligner maps 0 reads to multiple loci, but 3.7% to too many loci - meaning?
STAR
RNA-Seq
mapping
updated 5.4 years ago by
h.mon
35k • written 5.4 years ago by
Anand Rao
▴ 640
2
votes
2
replies
931
views
List of plant long read genome assemblies
plant
genome
long read
Assembly
5.4 years ago by
Anand Rao
▴ 640
1
vote
2
replies
1.5k
views
Multiple sequence alignment statistics
MSA
statistics
updated 5.6 years ago by
Biostar
20 • written 5.7 years ago by
Anand Rao
▴ 640
1
vote
3
replies
2.9k
views
Using row order of one heatmap for a new heatmap
Heatmap
R
row reorder
plot
5.6 years ago by
Anand Rao
▴ 640
1
vote
8
replies
1.5k
views
How can I perform pairwise comparison of protein secondary structure?
secondary structure
protein
structure alignment
updated 5.6 years ago by
Mensur Dlakic
★ 28k • written 5.6 years ago by
Anand Rao
▴ 640
3
votes
1
reply
1.5k
views
Evaluating protein structure predictions
protein structure
evaluation
ProQ
QMEAN
updated 5.6 years ago by
jgreener
▴ 390 • written 5.6 years ago by
Anand Rao
▴ 640
0
votes
1
reply
1.3k
views
RepeatModeler contig size filter and parallelization
RepeatModeler
Contig length
Parallel
5.9 years ago by
Anand Rao
▴ 640
0
votes
0
replies
1.7k
views
RepeatModeler run error troubleshooting
RepeatModeler
RepeatMasker
BuildDatabase
blastdb
5.9 years ago by
Anand Rao
▴ 640
0
votes
0
replies
1.4k
views
Extract VCF from genome assemblies of multiple individuals
SNP
Structural Variation
VCF
Genomes alignment
6.0 years ago by
Anand Rao
▴ 640
2
votes
6
replies
1.8k
views
Which NGS aligner to find inexact matches
DNA alignment
NGS aligner
genome coordinates
NGS
6.0 years ago by
Anand Rao
▴ 640
4
votes
4
replies
2.7k
views
bedtools subtract still overlaps by 1bp?
bedtools
getfasta
slop
subtract
updated 6.0 years ago by
finswimmer
16k • written 6.0 years ago by
Anand Rao
▴ 640
1
vote
1
reply
3.4k
views
Choosing tool for DNA secondary structure stem-loop prediction
secondary
stem loop
DNA
software
6.1 years ago by
Anand Rao
▴ 640
20
votes
4
replies
11k
views
Bulk download of entire BioProject SRA
SRA
NCBI
sratoolkit
entrez utilities
BioProject
updated 6.1 years ago by
Arup Ghosh
3.3k • written 6.1 years ago by
Anand Rao
▴ 640
12
votes
2
replies
4.2k
views
Visualize multiple GFF files
GFF
overlap
statistics
visualization
updated 6.1 years ago by
Joe
22k • written 6.5 years ago by
Anand Rao
▴ 640
4
votes
2
replies
5.0k
views
mummerplot for genome self alignment NOT yielding full length diagonal graph
mummer
nucmer
mummerplot
genome alignment
6.1 years ago by
Anand Rao
▴ 640
3
votes
5
replies
2.3k
views
CD-HIT results without sorting by length
clustering
CD-HIT
sort
length
6.1 years ago by
Anand Rao
▴ 640
2
votes
5
replies
1.7k
views
Merge intervals between but NOT within 2 BED files
bedtools
merge
overlap
bedops
updated 6.4 years ago by
Alex Reynolds
36k • written 6.4 years ago by
Anand Rao
▴ 640
1
vote
3
replies
1.8k
views
bedtools strategy to report both merged AND unmerged intervals
bedtools
merge
unmerged
gff3
6.5 years ago by
Anand Rao
▴ 640
0
votes
0
replies
1.5k
views
AUGUSTUS protein profile run error
augustus
ppx
error
6.6 years ago by
Anand Rao
▴ 640
2
votes
2
replies
1.2k
views
collapsing GFF coordinates with common start OR stop
GFF
parse
script
bedtools
Perl
updated 6.6 years ago by
h.mon
35k • written 6.6 years ago by
Anand Rao
▴ 640
8
votes
4
replies
5.4k
views
SPAdes assembler k-mer > default 127 possible?
Genome assembly
SPAdes
k-mer
updated 6.8 years ago by
ikangkim
▴ 50 • written 7.5 years ago by
Anand Rao
▴ 640
11
votes
10
replies
6.6k
views
Best mapping software to generate BAM file
BAM
mapping
updated 7.2 years ago by
Biostar
20 • written 7.4 years ago by
Anand Rao
▴ 640
0
votes
0
replies
1.5k
views
Simulating Core / Accessory genome for incomplete genome assemblies
Core
Accessory
Simulation
Incomplete draft
7.4 years ago by
Anand Rao
▴ 640
3
votes
3
replies
2.7k
views
Assess and correct any GC bias in Illumina HiSeq 4000 data
GC bias
Illumina
HiSeq 4000
coverage depth
updated 7.4 years ago by
Brian Bushnell
20k • written 7.4 years ago by
Anand Rao
▴ 640
9
votes
3
replies
8.1k
views
Illumina R1 vs. R2 read quality differences - reasons?
read quality
illumina
PE
updated 7.4 years ago by
Istvan Albert
102k • written 7.4 years ago by
Anand Rao
▴ 640
0
votes
0
replies
1.6k
views
ALLPATHS-LG error correction Perl script run error
ALLPATHS-LG
error correction
Perl
run error
updated 7.4 years ago by
Biostar
20 • written 7.5 years ago by
Anand Rao
▴ 640
7
votes
4
replies
4.8k
views
How to measure NGS depth coverage bias
NGS
Illumina
sequencing depth coverage
bias
updated 7.4 years ago by
Len Trigg
★ 1.6k • written 7.4 years ago by
Anand Rao
▴ 640
1
vote
1
reply
2.3k
views
REAPR run error
REAPR
SMALT
run error
7.4 years ago by
Anand Rao
▴ 640
0
votes
1
reply
1.7k
views
a5miseq syntax help
a5miseq
syntax
Fastq format
custom adapters
updated 7.4 years ago by
GenoMax
149k • written 7.4 years ago by
Anand Rao
▴ 640
1
vote
0
replies
2.7k
views
A5 pipeline begin and end
A5 pipeline
genome assembly
assembler
7.5 years ago by
Anand Rao
▴ 640
0
votes
2
replies
1.5k
views
a5pipeline.pl run error
a5_pipeline.pl
run error
phred encoding
7.5 years ago by
Anand Rao
▴ 640
0
votes
0
replies
1.4k
views
Aligning gene sequences
Splice-aware
Gene alignment
Exon-Intron boundary
7.5 years ago by
Anand Rao
▴ 640
79 results • Page
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