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Showing :
questions
0
votes
6
replies
569
views
PacBio adapters in transcriptome assembly from short read data?
adapter
transcriptome
sequencing
pacbio
vecscreen
15 days ago by
Dunois
★ 2.5k
0
votes
4
replies
829
views
Distinguishing between gene duplication and variation
sequence-analysis
16 months ago by
Dunois
★ 2.5k
3
votes
3
replies
702
views
NCBI esearch results inconsistent with web-based search results?
NCBI
eutils
updated 17 months ago by
GenoMax
141k • written 17 months ago by
Dunois
★ 2.5k
7
votes
4
replies
1.9k
views
AlphaFold 2 alternatives
protein-structure
alphafold
updated 28 days ago by
Ram
43k • written 17 months ago by
Dunois
★ 2.5k
3
votes
8
replies
1.2k
views
Improving existing genome with new RNA-seq data
annotatation
genome
RNA-seq
assembly
18 months ago by
Dunois
★ 2.5k
1
vote
4
replies
865
views
Bulk RNA-seq time course data with unknown sample sizes?
series
time
RNA-seq
normalization
transcriptomics
course
17 months ago by
Dunois
★ 2.5k
6
votes
10
replies
2.6k
views
What to do with a bunch of AlphaFold2 structures?
prediction
comparison
pymol
structure
alphafold2
updated 2.1 years ago by
Jiyao Wang
▴ 370 • written 2.7 years ago by
Dunois
★ 2.5k
0
votes
1
reply
740
views
Sequence search parameters for annotation of de novo transcriptomes
annotation
transcriptome
search
blast
updated 2.7 years ago by
Sej Modha
5.3k • written 2.7 years ago by
Dunois
★ 2.5k
1
vote
2
replies
712
views
Pooling annotations from different databases in InterProScan
annotations
interproscan
protein
sequence
domain
2.7 years ago by
Dunois
★ 2.5k
7
votes
5
replies
1.2k
views
Orthology, sequence similarity, and conservation of function
homology
function
similarity
prediction
sequence
orthology
2.7 years ago by
Dunois
★ 2.5k
2
votes
2
replies
697
views
Helper packages for differential gene expression analysis in R
dge
deseq2
RNA-seq
r
updated 2.8 years ago by
GenoMax
141k • written 2.8 years ago by
Dunois
★ 2.5k
0
votes
2
replies
690
views
Functional sub-grouping of orthogroup sequences
orthology
2.8 years ago by
Dunois
★ 2.5k
1
vote
1
reply
1.1k
views
Downloading the RefSeq proteins complete data set
ftp
refseq
updated 2.8 years ago by
GenoMax
141k • written 2.8 years ago by
Dunois
★ 2.5k
0
votes
0
replies
772
views
Choosing an outgroup for analyses with OrthoFinder
orthologs
phylogeny
outgroup
orthofinder
2.8 years ago by
Dunois
★ 2.5k
11
votes
8
replies
2.2k
views
PHRED scores and sequence errors
sequencing-errors
probability
PHRED
updated 11 months ago by
Ram
43k • written 2.9 years ago by
Dunois
★ 2.5k
1
vote
4
replies
908
views
Header conflicts in concatenated FASTQ file?
FASTQ
RNA-seq
concatenate
2.9 years ago by
Dunois
★ 2.5k
6
votes
7
replies
1.7k
views
Assessing read support for coding sequences predicted by TransDecoder
cds prediction
transdecoder
de novo assembly
updated 3.0 years ago by
ponganta
▴ 590 • written 3.4 years ago by
Dunois
★ 2.5k
1
vote
6
replies
1.4k
views
Redundancy reduction of de novo transcriptome assemblies with Compacta?
de-novo
transcriptome
redundancy-reduction
3.0 years ago by
Dunois
★ 2.5k
6
votes
11
replies
1.8k
views
How are transcriptome annotations published?
RNAseq
annotation
publish
transcriptome
2.8 years ago by
Dunois
★ 2.5k
2
votes
1
reply
820
views
Orthology and sequence identity/similarity
identity
similarity
orthology
homology
updated 3.1 years ago by
Mensur Dlakic
★ 27k • written 3.1 years ago by
Dunois
★ 2.5k
0
votes
0
replies
674
views
Why does KAAS use SBH for partial genomes?
orthology
blast
reciprocal best hit
annotation
3.2 years ago by
Dunois
★ 2.5k
1
vote
1
reply
653
views
Create pseudo-replicates by "evenly" splitting reads file?
RNA-Seq
Assembly
paired-end
reads
3.2 years ago by
Dunois
★ 2.5k
3
votes
6
replies
1.4k
views
Why do the number of domains in these two orthologs differ? Why is hmmscan annotating one of these sequences incorrectly?
orthology
pfam
hmmer
annotation
domains
updated 3.2 years ago by
Mensur Dlakic
★ 27k • written 3.2 years ago by
Dunois
★ 2.5k
1
vote
1
reply
964
views
How to sort a FASTA file and (its) BAM file in the same order?
fasta
bam
samtools
3.3 years ago by
Dunois
★ 2.5k
3
votes
2
replies
667
views
What proportion of the (coding) genome is actually expressed at any given time?
genome
gene expression
RNA-Seq
updated 3.3 years ago by
GenoMax
141k • written 3.3 years ago by
Dunois
★ 2.5k
0
votes
3
replies
4.1k
views
Help interpret features in fastp insert size and sequence quality plots
RNA-Seq
fastp
quality control
sequencing
3.3 years ago by
Dunois
★ 2.5k
7
votes
7
replies
2.2k
views
MD5 checksums of two "identical" Gzipped fastq files different?
checksum
RNA-Seq
fastq
integrity
updated 3.4 years ago by
Pierre Lindenbaum
161k • written 3.4 years ago by
Dunois
★ 2.5k
7
votes
5
replies
916
views
Where/how do proteins with "-like" in their names get their names?
protein
nomenclature
homology
3.4 years ago by
Dunois
★ 2.5k
0
votes
2
replies
1.4k
views
Remote blast with blast v2.10.1 not working
blast
software error
updated 3.4 years ago by
Biostar
20 • written 3.6 years ago by
Dunois
★ 2.5k
11
votes
34
replies
2.2k
views
De novo transcriptome from PE reads with high multi-mapping rate (Bowtie2)
RNA-Seq
read support
Assembly
bowtie2
3.6 years ago by
Dunois
★ 2.5k
4
votes
2
replies
2.6k
views
Gibbs sampling/bootstrap replicates in Salmon
salmon
uncertainty
updated 3.6 years ago by
Rob
6.5k • written 3.6 years ago by
Dunois
★ 2.5k
1
vote
2
replies
803
views
Looking for raw, unprocessed RNA-seq datasets
rna-seq
dataset
raw reads
data
3.6 years ago by
Dunois
★ 2.5k
0
votes
6
replies
1.2k
views
Cleaning/filtering RNA seq reads from novel species
RNA-Seq
sequencing
Assembly
denovo
updated 3.6 years ago by
Biostar
20 • written 3.7 years ago by
Dunois
★ 2.5k
0
votes
17
replies
1.5k
views
Transcripts with no read support
RNA-Seq
alignment
assembly
salmon
3.6 years ago by
Dunois
★ 2.5k
0
votes
2
replies
1.0k
views
Alternatives to Transrate
Assembly
RNA-Seq
quality control
evaluation
updated 3.7 years ago by
Biostar
20 • written 3.7 years ago by
Dunois
★ 2.5k
0
votes
9
replies
696
views
Transcriptome-based species identification
RNA-Seq
species identification
blast
alignment
updated 3.7 years ago by
Biostar
20 • written 3.7 years ago by
Dunois
★ 2.5k
36 results • Page
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