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Showing :
questions
3
votes
6
replies
1.2k
views
Other databases for deposition of scRNA-seq data than NCBI GEO?
database
scRNA
2.4 years ago by
mschmid
▴ 180
0
votes
0
replies
359
views
Open Source replacement for MatInspector (prediction transcription factor binding sites)
transcription-factor
2.5 years ago by
mschmid
▴ 180
0
votes
1
reply
1.9k
views
Blastn: In The Scoring Parameters, What Does "Linear" Mean?
blastn
alignment
updated 3.2 years ago by
Biostar
20 • written 10.1 years ago by
mschmid
▴ 180
0
votes
2
replies
2.1k
views
How to retrieve all hmm from TIGRFAM for Cas (CRISPR-associated) proteins?
hmm
Cas
CRISPR
updated 4.1 years ago by
Biostar
20 • written 7.1 years ago by
mschmid
▴ 180
4
votes
4
replies
722
views
Which human chromosome would you use to generate a "toy data set"
sequencing
genome
4.3 years ago by
mschmid
▴ 180
0
votes
1
reply
770
views
Mimicing the Blastn "lineage report" from online Blast service
blast
4.5 years ago by
mschmid
▴ 180
0
votes
1
reply
975
views
How to get all Blastn hits
blastn
4.5 years ago by
mschmid
▴ 180
4
votes
7
replies
1.4k
views
Visualize short nucleotide sequences and some ranges on top
visualization
bed
gff
updated 4.6 years ago by
bernatgel
★ 3.4k • written 4.6 years ago by
mschmid
▴ 180
6
votes
1
reply
788
views
Detect repeats problematic for PCR
prc
repeats
4.6 years ago by
mschmid
▴ 180
2
votes
1
reply
1.5k
views
Get Gene Onthology information for NCBI GeneIDs - Apis mellifera (honey bee)
RNA-Seq
GO-Enrichment
updated 4.6 years ago by
Kevin Blighe
87k • written 4.6 years ago by
mschmid
▴ 180
0
votes
1
reply
902
views
DESeq2 -- Three conditions with "gradient"
DESeq2
RNA-Seq
updated 4.6 years ago by
swbarnes2
14k • written 4.6 years ago by
mschmid
▴ 180
1
vote
5
replies
969
views
dUTP sequencing -- different strand-ratios for different samples
rna-seq
dUTP
HISAT2
updated 4.6 years ago by
Charles Warden
8.2k • written 4.6 years ago by
mschmid
▴ 180
3
votes
5
replies
1.2k
views
Would you remove rRNA reads in silico before testing for diff. expression?
RNA-Seq
4.6 years ago by
mschmid
▴ 180
0
votes
2
replies
886
views
Coloring nucleotide sequences according to their GC content
sequence
4.6 years ago by
mschmid
▴ 180
1
vote
2
replies
2.1k
views
SMRT analysis- what is difference between RS_HGAP_Assembly.2 vs RS_HGAP_Assembly.3
pacbio
assembly
updated 21 months ago by
Ram
43k • written 8.4 years ago by
mschmid
▴ 180
2
votes
3
replies
1.7k
views
ClustalO computing suboptimal alignment
alignment
clustalomega
5.0 years ago by
mschmid
▴ 180
0
votes
2
replies
898
views
Where to find a list of (sequenced) WHO reference strains
genome
5.1 years ago by
mschmid
▴ 180
2
votes
3
replies
1.0k
views
What does 1V1 exactly mean?
alignment
polishing
updated 5.1 years ago by
ATpoint
82k • written 5.1 years ago by
mschmid
▴ 180
3
votes
1
reply
1.8k
views
JGI databases vs GenBank
ncbi
jgi
img
updated 5.2 years ago by
Juke34
8.6k • written 5.2 years ago by
mschmid
▴ 180
2
votes
11
replies
1.4k
views
Majority of genes upregulated in RNA-seq study of toxic compound
RNA-Seq
updated 5.4 years ago by
Benn
8.3k • written 5.4 years ago by
mschmid
▴ 180
0
votes
2
replies
1.7k
views
Get aligment quality / identity from CRAM file (for PacBio and ONT data)
PacBio
ONT
cram
alignment quality
6.2 years ago by
mschmid
▴ 180
0
votes
0
replies
1.4k
views
Is it useful to calculate profile hmm from core genome clusters?
genome
gene
updated 6.8 years ago by
Biostar
20 • written 6.9 years ago by
mschmid
▴ 180
0
votes
1
reply
1.5k
views
GO enrichment analysis for pseudogenes in bacterium
gene
genome
updated 6.9 years ago by
dago
★ 2.8k • written 6.9 years ago by
mschmid
▴ 180
1
vote
1
reply
1.7k
views
Get all bacterial protein sequences from Genbank but non redundant
ncbi
bacteria
protein
6.9 years ago by
mschmid
▴ 180
0
votes
1
reply
1.1k
views
Link methylation patterns to restriction enzymes
methylation
PacBio
7.1 years ago by
mschmid
▴ 180
0
votes
1
reply
1.4k
views
Pan- / coregenome studies - exclude plasmids?
comparative genomics
pan/coregenome
7.1 years ago by
mschmid
▴ 180
3
votes
1
reply
1.6k
views
Draw phylogenetic tree with zoom into a specific clade
phylogeny
updated 7.2 years ago by
Pierre Lindenbaum
161k • written 7.2 years ago by
mschmid
▴ 180
0
votes
0
replies
1.4k
views
Who has tried bcgTree - Comments?
core genome
aligment
phylogeny
7.2 years ago by
mschmid
▴ 180
0
votes
1
reply
1.2k
views
bwa: get all aligment positions of a read
bwa
mapping
7.2 years ago by
mschmid
▴ 180
0
votes
6
replies
2.4k
views
bbmap: Order of reference genomes seems to matter
bbmap
mapping
illumina
7.2 years ago by
mschmid
▴ 180
0
votes
3
replies
2.7k
views
Find telomeres and centromeres in de novo sequenced fungi
genome
updated 7.2 years ago by
EagleEye
7.5k • written 8.2 years ago by
mschmid
▴ 180
2
votes
7
replies
4.8k
views
All vs. all pairwise sequence aligment
alignment
local
fasta
updated 7.2 years ago by
kloetzl
★ 1.1k • written 7.2 years ago by
mschmid
▴ 180
2
votes
4
replies
1.7k
views
samtoroc.sh -- no truePositive hits
bbmap
illumina
roc
updated 7.3 years ago by
Brian Bushnell
20k • written 7.3 years ago by
mschmid
▴ 180
2
votes
6
replies
1.6k
views
How to further investigate into genomic island with only hypothetical proteins
annotation
genomic island
bacteria
updated 7.3 years ago by
Michael
54k • written 7.3 years ago by
mschmid
▴ 180
2
votes
1
reply
1.5k
views
Database for Antibiotic/Antimicrobial products of Bacteria
database
antibiotic
updated 7.7 years ago by
Biostar
20 • written 8.4 years ago by
mschmid
▴ 180
4
votes
2
replies
2.2k
views
Correct substitution model for yeast - RAxML
raxml
substitution model
tree
updated 7.8 years ago by
Sej Modha
5.3k • written 7.8 years ago by
mschmid
▴ 180
1
vote
1
reply
1.8k
views
BioPython: How to set the order of qualifiers
Genbank
biopython
updated 7.8 years ago by
Peter
6.0k • written 7.9 years ago by
mschmid
▴ 180
0
votes
1
reply
1.6k
views
What is limiting the read size of Pacbio SMRT sequencing
NGS
pacbio
readlength
8.0 years ago by
mschmid
▴ 180
3
votes
1
reply
1.3k
views
Find occurrence of short pattern in fasta with several sequences and ouput it to bam
alignment
updated 8.2 years ago by
Sean Davis
26k • written 8.2 years ago by
mschmid
▴ 180
2
votes
5
replies
2.2k
views
How to judge severity of variants in genes
variants
SNP
annotation
updated 21 months ago by
Ram
43k • written 8.5 years ago by
mschmid
▴ 180
0
votes
0
replies
2.2k
views
How to find pseudogenes in bacteria
annotation
updated 21 months ago by
Ram
43k • written 8.3 years ago by
mschmid
▴ 180
1
vote
3
replies
2.2k
views
Is there any pairing info Genome <-> Plasmid in Genbank available?
genbank
genome
plasmid
updated 20 months ago by
Ram
43k • written 8.5 years ago by
mschmid
▴ 180
4
votes
4
replies
2.4k
views
Where to put start for assembled genome/plasmid
Assembly
genome
sequencing
updated 20 months ago by
Ram
43k • written 8.6 years ago by
mschmid
▴ 180
2
votes
9
replies
3.8k
views
Is this mate pair insert size distribution to broad?
spades
illumina
mate-pair
updated 20 months ago by
Ram
43k • written 8.6 years ago by
mschmid
▴ 180
8
votes
3
replies
2.4k
views
Illumina PE - what are causes for coverage drops?
illumina
coverage
paired end
updated 8.6 years ago by
thackl
★ 3.0k • written 8.6 years ago by
mschmid
▴ 180
2
votes
2
replies
2.0k
views
Assemble mix of two plasmids which have partially similar sequence
illumina
Assembly
spades
plasmids
updated 19 months ago by
Ram
43k • written 8.6 years ago by
mschmid
▴ 180
0
votes
2
replies
4.5k
views
Where to get some example metagenomics data?
metagenomics
database
updated 19 months ago by
Ram
43k • written 8.7 years ago by
mschmid
▴ 180
3
votes
4
replies
2.7k
views
How to get subset from NCBI databases using Accession/GI
NCBI
blast
database
updated 19 months ago by
Ram
43k • written 8.7 years ago by
mschmid
▴ 180
1
vote
2
replies
2.6k
views
Nice open source alternative to "contig viewer" in SeqMan Pro
SeqMan
contig
paired end
updated 8.7 years ago by
Lesley Sitter
▴ 600 • written 8.7 years ago by
mschmid
▴ 180
4
votes
4
replies
5.0k
views
Trim Illumina PE data with trimmomatic
trimming
sequencing
paired-end
illumina
updated 19 months ago by
Ram
43k • written 8.7 years ago by
mschmid
▴ 180
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