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questions
1
vote
7
replies
544
views
fastp - can I trim specific adapters only?
trimming
fastp
adapter
5 weeks ago by
liorglic
★ 1.4k
2
votes
4
replies
925
views
Repeat detection/masking in bacteria
annotation
repeat-masking
updated 7 months ago by
Max Sikolenko
• 0 • written 10 months ago by
liorglic
★ 1.4k
1
vote
2
replies
543
views
Differential gene expression with specif genes of interest
RNA-seq
DGE
updated 9 months ago by
Zhenyu Zhang
★ 1.2k • written 9 months ago by
liorglic
★ 1.4k
3
votes
2
replies
756
views
High-resolution annotation of LTR elements
LTR
updated 14 months ago by
colindaven
6.4k • written 15 months ago by
liorglic
★ 1.4k
1
vote
4
replies
1.5k
views
Repeat masking for genome annotation
masking
annotation
repeat
14 months ago by
liorglic
★ 1.4k
0
votes
0
replies
387
views
Statistical test on two phylogenetically remote groups
phylogeny
ANOVA
15 months ago by
liorglic
★ 1.4k
8
votes
5
replies
1.3k
views
Classifying repeat features from Ensembl
ensembl
repeat
updated 5 weeks ago by
e.r.zakiev
▴ 210 • written 16 months ago by
liorglic
★ 1.4k
3
votes
1
reply
553
views
Quickly examining many MSAs
MSA
updated 18 months ago by
Dave Carlson
★ 1.7k • written 18 months ago by
liorglic
★ 1.4k
0
votes
2
replies
746
views
SNP calling from plant whole genome assemblies
calling
snp
whole
assembly
genome
22 months ago by
liorglic
★ 1.4k
0
votes
2
replies
1.0k
views
vg for gene presence-absence analysis
vg
pan-genome
vgteam
PAV
graph
variation
2.1 years ago by
liorglic
★ 1.4k
2
votes
2
replies
898
views
Unable to parse Open Tree of Life Newick with ete3 (python)
newick
python
ete3
updated 2.1 years ago by
Joe
21k • written 2.1 years ago by
liorglic
★ 1.4k
0
votes
4
replies
704
views
DGE - command line alternatives to R packages?
DGE
CLI
RNA-seq
R
updated 2.2 years ago by
LauferVA
4.2k • written 2.2 years ago by
liorglic
★ 1.4k
1
vote
2
replies
613
views
Running Galaxy tools on a HPC cluster using CLI?
galaxy
HPC
updated 2.2 years ago by
Wayne
★ 2.0k • written 2.2 years ago by
liorglic
★ 1.4k
1
vote
2
replies
632
views
NGS sequencing depth notation
NGS
depth
updated 2.3 years ago by
Istvan Albert
100k • written 2.3 years ago by
liorglic
★ 1.4k
1
vote
3
replies
997
views
Clumpify on multiple files
dedupe
clumpify
fastq
2.3 years ago by
liorglic
★ 1.4k
1
vote
3
replies
780
views
Data sets of WGS + disease phenotypes?
wgs
phenotype
updated 2.4 years ago by
abedkurdi10
▴ 190 • written 2.4 years ago by
liorglic
★ 1.4k
0
votes
0
replies
502
views
Better assembly results with lower depth !?
megahit
assembly
2.4 years ago by
liorglic
★ 1.4k
1
vote
3
replies
928
views
BAM - number of mapping positions per read
sam
bwa
bowtie
bam
2.5 years ago by
liorglic
★ 1.4k
1
vote
1
reply
1.3k
views
Using Aspera to download from GSA (BIG)
Aspera
GSA
updated 14 months ago by
Ram
43k • written 3.5 years ago by
liorglic
★ 1.4k
0
votes
1
reply
654
views
Using protein domains for annotation validation
Interpro
annotation
domain
InterproScan
updated 2.8 years ago by
Jean-Karim Heriche
27k • written 2.8 years ago by
liorglic
★ 1.4k
2
votes
5
replies
1.7k
views
Weird characters in yeast reference gff3
SGD
gff3
yeast
gff
2.9 years ago by
liorglic
★ 1.4k
3
votes
11
replies
1.6k
views
Simple genome annotation using transcripts data
annotation
fasta
gff
updated 3.0 years ago by
sagnik
▴ 50 • written 3.9 years ago by
liorglic
★ 1.4k
0
votes
0
replies
455
views
How to handle mis-annotated chimeric genes?
chimeric
MAKER
curation
annotation
3.1 years ago by
liorglic
★ 1.4k
3
votes
6
replies
4.0k
views
Is the ENSEMBL FTP down?
ensembl
ftp
updated 2.7 years ago by
rohitsatyam102
▴ 870 • written 3.2 years ago by
liorglic
★ 1.4k
1
vote
10
replies
5.2k
views
6 follow
IGV memory on Windows
igv
gff
updated 3.4 years ago by
Noah
▴ 10 • written 4.1 years ago by
liorglic
★ 1.4k
1
vote
2
replies
1.2k
views
Is ENA API down?
ena
3.4 years ago by
liorglic
★ 1.4k
4
votes
7
replies
1.2k
views
blastn much slower on longer subject sequences?
blast
blastn
updated 3.8 years ago by
JC
13k • written 3.8 years ago by
liorglic
★ 1.4k
1
vote
0
replies
711
views
Selecting samples from a VCF that best represent population variation
vcf
3.8 years ago by
liorglic
★ 1.4k
2
votes
11
replies
1.3k
views
Sequence clustering tool that can break sequences?
clustering
3.9 years ago by
liorglic
★ 1.4k
2
votes
2
replies
2.8k
views
PLINK - Sample(s) present with no genotype data
plink
updated 4.1 years ago by
chrchang523
10k • written 4.1 years ago by
liorglic
★ 1.4k
0
votes
1
reply
628
views
What happens during Blast DB creation?
blast
4.2 years ago by
liorglic
★ 1.4k
0
votes
0
replies
784
views
Determining reason for low quality assembly
Assembly
spades
4.2 years ago by
liorglic
★ 1.4k
5
votes
4
replies
1.6k
views
DELLY produces empty output
delly
cnv
sv
4.2 years ago by
liorglic
★ 1.4k
2
votes
7
replies
2.8k
views
Low percent of RNA-seq reads mapping
RNA-Seq
STAR
mapping
updated 4.3 years ago by
Amitm
★ 2.2k • written 4.3 years ago by
liorglic
★ 1.4k
0
votes
2
replies
567
views
Proportion of long-read sequencing out of all sequencing?
long reads
4.4 years ago by
liorglic
★ 1.4k
2
votes
4
replies
1.5k
views
How to handle paralogs in pan-genomes?
orthologs
paralogs
pan-genome
4.4 years ago by
liorglic
★ 1.4k
0
votes
2
replies
781
views
Assigning proteins to pre-computed gene families
gene family
Ensembl
Phytozome
updated 4.4 years ago by
Mensur Dlakic
★ 27k • written 4.4 years ago by
liorglic
★ 1.4k
1
vote
7
replies
1.5k
views
QUAST ignoring bam files
QUAST
4.4 years ago by
liorglic
★ 1.4k
2
votes
3
replies
1.2k
views
How to group genes in a single genome into gene families?
gene family
updated 4.5 years ago by
Renesh
★ 2.2k • written 4.5 years ago by
liorglic
★ 1.4k
0
votes
1
reply
728
views
Inference of gene content evolution within a phylogeny
gene
updated 4.7 years ago by
andres.firrincieli
3.6k • written 4.7 years ago by
liorglic
★ 1.4k
2
votes
4
replies
1.9k
views
A software tool for gene copy number and loss detection
genome
updated 4.8 years ago by
Costadia
▴ 10 • written 4.8 years ago by
liorglic
★ 1.4k
2
votes
6
replies
4.9k
views
Reference-guided assembly from short reads
assembly
ngs
5.0 years ago by
liorglic
★ 1.4k
3
votes
3
replies
1.7k
views
What's the right way to submit a genome assembly to NCBI?
Assembly
5.3 years ago by
liorglic
★ 1.4k
1
vote
5
replies
4.2k
views
Merging multiple sets of transcripts (generated by Trinity)
Assembly
RNA-Seq
5.9 years ago by
liorglic
★ 1.4k
0
votes
3
replies
1.8k
views
extract one-side unmapped reads from sam
sam
bam
samtools
tophat
updated 5.9 years ago by
Carlo Yague
8.7k • written 5.9 years ago by
liorglic
★ 1.4k
0
votes
0
replies
2.3k
views
cDNA/EST/Random library selection for transcriptome assembly
RNA-Seq
cDNA
EST
sequencing
assembly
6.0 years ago by
liorglic
★ 1.4k
3
votes
8
replies
2.0k
views
RNA-seq data for de-novo transcript assembly
rna
RNA-Seq
rna-seq
Assembly
assembly
updated 6.2 years ago by
lieven.sterck
15k • written 6.2 years ago by
liorglic
★ 1.4k
1
vote
3
replies
1.3k
views
Strategy for genome annotation for a new individual of a well-established species
Assembly
annotation
transcriptome
updated 6.2 years ago by
Rohit
★ 1.5k • written 6.2 years ago by
liorglic
★ 1.4k
3
votes
4
replies
2.7k
views
Gene copies vs. gene paralogs - what's the difference
CNV
paralogs
WGS
updated 6.4 years ago by
Emily
23k • written 6.4 years ago by
liorglic
★ 1.4k
1
vote
1
reply
1.6k
views
Genome annotation tools - current status. Machine learning?
genome
Assembly
annotation
machine learning
updated 7.4 years ago by
prash
▴ 10 • written 7.4 years ago by
liorglic
★ 1.4k
52 results • Page
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