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1
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The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Primers TRINITY
11 days ago by mathavanbioinfo ▴ 90
0
votes
1
reply
290
views
What alternative method would recommend for conducting gene ontology analysis?
WEGO gene-ontology
updated 5 weeks ago by ★ 1.9k • written 5 weeks ago by ▴ 90
1
vote
3
replies
805
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Can shotgun metagenome approaches effectively target both RNA and DNA viruses in low-viral-load water samples?
RNA-virus binning metagenome abundance shotgun
updated 5 weeks ago by ▴ 580 • written 5 weeks ago by ▴ 90
4
votes
1
reply
280
views
why there is an asterisk symbol at the end of each proteins sequences of fasta files in the Braker3 output?
gtf breaker3 protein-seq
6 weeks ago by mathavanbioinfo ▴ 90
4
votes
4
replies
366
views
Is it feasible to merge Illumina RNA-Seq data with varying read lengths?
illumina RNA-seq paired-end
updated 7 weeks ago by 19k • written 7 weeks ago by ▴ 90
0
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0
replies
200
views
Gene Prediction Breaker3
prediction protein-seq GTF Breaker3 gene
7 weeks ago by mathavanbioinfo ▴ 90
1
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1
reply
792
views
What is the data requirement for shotgun metagenome analysis of soil samples from plastic land-filling, coal mining, and petroleum oil refineries fie…
shotgun-metagenome species-level binning gtdbk data-requirement
updated 3 months ago by 141k • written 3 months ago by ▴ 90
1
vote
1
reply
245
views
Genome Analysis Insights: BUSCO Evaluation of Repetitive Elements and Ploidy Level in Crocus sativus"
coverage ploidy complex-genome BUSCO
updated 3 months ago by 43k • written 3 months ago by ▴ 90
2
votes
3
replies
1.2k
views
How to identify the 300 kb upstream and downstream genes of lncRNAs?
RNA-Seq lncRNA target genes upstream downstream
updated 5 months ago by • 0 • written 3.4 years ago by ▴ 90
0
votes
1
reply
525
views
How to remove cloning vector sequence from bacterial assembled genome?
assembly removal bacterial genome vector
updated 10 months ago by 141k • written 10 months ago by ▴ 90
3
votes
2
replies
897
views
How interpret question mark symbol strand column in GFF file?
GFF transcriptome
updated 17 months ago by 14k • written 17 months ago by ▴ 90
2
votes
1
reply
451
views
How to run phylogeny for genome assembly file?
phylogenetic tree Phylogeny assembly genome
updated 19 months ago by ★ 27k • written 19 months ago by ▴ 90
1
vote
2
replies
548
views
How to download all fungal virulence proteins from UniProt?
protein blast fungi uniprot
updated 13 months ago by 43k • written 20 months ago by ▴ 90
1
vote
1
reply
516
views
Differential Gene Expression of lncRNAs analysis from GENCODE reference file?
DEG lncRNA
updated 21 months ago by ★ 1.9k • written 21 months ago by ▴ 90
0
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0
replies
327
views
How to merge the pair end sample for GBS analysis in TASSEL software?
GBS plot GAPPIT
updated 2.0 years ago by 8.7k • written 2.0 years ago by ▴ 90
1
vote
1
reply
753
views
Subread FeatureCounts produces zero percent successfull alignment
zero subread featrureCounts alignment
updated 2.3 years ago by 8.7k • written 2.3 years ago by ▴ 90
0
votes
1
reply
951
views
Unable to download kraken2 database
databaase kraken2 metagenome
updated 2.3 years ago by 141k • written 2.3 years ago by ▴ 90
0
votes
0
replies
476
views
How to remove the isoform in the trasncript.fa file from salmon output?
transcript salmon denovo assembly
updated 2.4 years ago by 82k • written 2.4 years ago by ▴ 90
0
votes
1
reply
1.2k
views
How to calculate phred score of fastq files?
linux phred fastq
updated 2.6 years ago by 141k • written 2.6 years ago by ▴ 90
0
votes
2
replies
868
views
How to download all the genome fasta file for plants?
standalone blast
updated 2.6 years ago by ★ 3.7k • written 2.6 years ago by ▴ 90
0
votes
0
replies
424
views
How to add enzyme details in Tassel pipeline?
GBS Tassel GBSEnzyme.java
updated 2.7 years ago by 5.8k • written 2.8 years ago by ▴ 90
4
votes
7
replies
3.0k
views
How to move the files from sub folder and sub-sub folders into one other folder?
bash
updated 13 months ago by 43k • written 2.8 years ago by ▴ 90
1
vote
1
reply
1.3k
views
what is the meaning of --dta paremeter used in the Hisat2 alignment?
Hisat2
updated 2.8 years ago by 43k • written 2.8 years ago by ▴ 90
0
votes
4
replies
812
views
extract the ids and key values
extract grep
updated 2.9 years ago by 8.6k • written 2.9 years ago by ▴ 90
6
votes
6
replies
1.8k
views
How to generate GTF file from BLAST output?
GTF
2.9 years ago by mathavanbioinfo ▴ 90
0
votes
1
reply
695
views
Where to get the human mitochondiral reference genome?
GTF human genome mitochondiral
updated 2.9 years ago by 141k • written 2.9 years ago by ▴ 90
3
votes
4
replies
1.3k
views
Proportion of RNAseq reads mapping to rRNA, tRNA, mRNA, and intergenic or antisense regions of the genome?
GTF featureCounts NGS GFF
updated 2.9 years ago by 19k • written 2.9 years ago by ▴ 90
0
votes
1
reply
685
views
How to view large PPI network in STRING database?
PPI large network STRING
updated 2.9 years ago by 27k • written 2.9 years ago by ▴ 90
0
votes
3
replies
1.1k
views
How can I get three letter organism code for cavia porcellus?
GO three KEGG
updated 3.0 years ago by 7.5k • written 3.0 years ago by ▴ 90
5
votes
3
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902
views
Where I can get the gtf file of antheraea mylitta
GTF
updated 3.0 years ago by 15k • written 3.0 years ago by ▴ 90
0
votes
0
replies
546
views
Extracting the genes associated drugs?
bank Drug
3.0 years ago by mathavanbioinfo ▴ 90
4
votes
5
replies
2.3k
views
How to download entire human protein sequences from RefSeq database hrough command line?
Refseq programming
updated 3.1 years ago by ★ 3.7k • written 3.1 years ago by ▴ 90
2
votes
2
replies
703
views
How to handle "perbase quality failed" issue?
RNA-Seq fastqc
3.4 years ago by mathavanbioinfo ▴ 90
4
votes
6
replies
3.1k
views
How to perform the lncRNA enrichment analysis?
lncRNA enrichment gene ontology
updated 3.4 years ago by ▴ 180 • written 3.5 years ago by ▴ 90
2
votes
1
reply
1.0k
views
How to extract upstream and downstream of lncRNA in particular range?
RNA-Seq lncRNA hommer bed gtf
updated 3.4 years ago by ▴ 480 • written 3.4 years ago by ▴ 90
1
vote
1
reply
663
views
How to find the gene name and classification using Ensembl ID?
genome ensembl lncRNA
updated 3.5 years ago by 27k • written 3.5 years ago by ▴ 90
1
vote
2
replies
1.2k
views
How create annotation file for WGCNA for RNA-Seq data?
RNA-Seq WGCNA Annotaion file
updated 3.8 years ago by 87k • written 3.8 years ago by ▴ 90
0
votes
1
reply
1.0k
views
How to make annotation file for WGCNA analysis of RNA Seq data?
next-gen
updated 4.1 years ago by 87k • written 4.1 years ago by ▴ 90
0
votes
2
replies
982
views
DEGS analysis with DESeq2?
DESeq2 DEGs
updated 4.1 years ago by 20 • written 4.2 years ago by ▴ 90
0
votes
0
replies
872
views
lncRNA prediction using CPAT?
CPAT lncRNA
4.1 years ago by mathavanbioinfo ▴ 90
0
votes
1
reply
797
views
DEGs analysis with StringTie results?
StringTie DEGs DESeq2
4.2 years ago by mathavanbioinfo ▴ 90
2
votes
8
replies
2.3k
views
How to get GTF file for Rousettus_aegyptiacus?
StringTie GTF Assembly Rousettus aegyptiacus
4.3 years ago by mathavanbioinfo ▴ 90
0
votes
1
reply
929
views
How to construct draft genome of virus using Trinity de novo assembler?
RNA virus amplicons trintiy
4.3 years ago by mathavanbioinfo ▴ 90
0
votes
4
replies
2.0k
views
How to extract 3', 5' UTR sequences from genbank records using python, PERL and R code?
UTR
updated 4.3 years ago by ▴ 120 • written 4.3 years ago by ▴ 90
0
votes
2
replies
743
views
Is virus specific UTR prediction tool available?
UTR
4.4 years ago by mathavanbioinfo ▴ 90
0
votes
0
replies
529
views
Best assembler for WGS for RNA viruses?
WGS
4.4 years ago by mathavanbioinfo ▴ 90
2
votes
1
reply
802
views
How to create matrix for larger data set?
matrix RNA-Seq
updated 4.6 years ago by 82k • written 4.6 years ago by ▴ 90
0
votes
0
replies
945
views
What is the differences in index building by hisat with or without exon, splicing variant files?
lncRNA RNA-Seq hisat2
4.6 years ago by mathavanbioinfo ▴ 90
0
votes
0
replies
1.5k
views
How to convert agilent probe id into gene symbol in gene expression matrix?
agilent probe conversion
4.6 years ago by mathavanbioinfo ▴ 90
0
votes
0
replies
807
views
Novel lncRNA identification and quantification RNA seq?
RNA-Seq sequencing assembly hisat2 lncRNA
4.6 years ago by mathavanbioinfo ▴ 90
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