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questions
0
votes
1
reply
295
views
How to remove cloning vector sequence from bacterial assembled genome?
assembly
removal
bacterial
genome
vector
updated 3 months ago by
GenoMax
134k • written 3 months ago by
mathavanbioinfo
▴ 70
3
votes
2
replies
645
views
How interpret question mark symbol strand column in GFF file?
GFF
transcriptome
updated 9 months ago by
dariober
14k • written 9 months ago by
mathavanbioinfo
▴ 70
2
votes
1
reply
327
views
How to run phylogeny for genome assembly file?
phylogenetic
tree
Phylogeny
assembly
genome
updated 12 months ago by
Mensur Dlakic
★ 24k • written 12 months ago by
mathavanbioinfo
▴ 70
1
vote
2
replies
376
views
How to download all fungal virulence proteins from UniProt?
protein
blast
fungi
uniprot
updated 6 months ago by
Ram
40k • written 13 months ago by
mathavanbioinfo
▴ 70
1
vote
1
reply
352
views
Differential Gene Expression of lncRNAs analysis from GENCODE reference file?
DEG
lncRNA
updated 14 months ago by
mark.ziemann
★ 1.8k • written 14 months ago by
mathavanbioinfo
▴ 70
0
votes
0
replies
239
views
How to merge the pair end sample for GBS analysis in TASSEL software?
GBS
plot
GAPPIT
updated 17 months ago by
Carlo Yague
8.4k • written 17 months ago by
mathavanbioinfo
▴ 70
1
vote
1
reply
594
views
Subread FeatureCounts produces zero percent successfull alignment
zero
subread
featrureCounts
alignment
updated 20 months ago by
Carlo Yague
8.4k • written 20 months ago by
mathavanbioinfo
▴ 70
0
votes
1
reply
713
views
Unable to download kraken2 database
databaase
kraken2
metagenome
updated 21 months ago by
GenoMax
134k • written 21 months ago by
mathavanbioinfo
▴ 70
0
votes
0
replies
354
views
How to remove the isoform in the trasncript.fa file from salmon output?
transcript
salmon
denovo
assembly
updated 21 months ago by
ATpoint
76k • written 21 months ago by
mathavanbioinfo
▴ 70
0
votes
1
reply
849
views
How to calculate phred score of fastq files?
linux
phred
fastq
updated 2.0 years ago by
GenoMax
134k • written 2.0 years ago by
mathavanbioinfo
▴ 70
0
votes
2
replies
717
views
How to download all the genome fasta file for plants?
standalone
blast
updated 2.0 years ago by
vkkodali_ncbi
★ 3.6k • written 2.0 years ago by
mathavanbioinfo
▴ 70
0
votes
0
replies
339
views
How to add enzyme details in Tassel pipeline?
GBS
Tassel
GBSEnzyme.java
updated 2.1 years ago by
lakhujanivijay
5.8k • written 2.2 years ago by
mathavanbioinfo
▴ 70
4
votes
7
replies
2.5k
views
How to move the files from sub folder and sub-sub folders into one other folder?
bash
updated 6 months ago by
Ram
40k • written 2.2 years ago by
mathavanbioinfo
▴ 70
1
vote
1
reply
991
views
what is the meaning of --dta paremeter used in the Hisat2 alignment?
Hisat2
updated 2.2 years ago by
Ram
40k • written 2.2 years ago by
mathavanbioinfo
▴ 70
0
votes
4
replies
641
views
extract the ids and key values
extract
grep
updated 2.2 years ago by
Juke34
8.2k • written 2.2 years ago by
mathavanbioinfo
▴ 70
6
votes
6
replies
1.4k
views
How to generate GTF file from BLAST output?
GTF
2.3 years ago by
mathavanbioinfo
▴ 70
0
votes
1
reply
566
views
Where to get the human mitochondiral reference genome?
GTF
human
genome
mitochondiral
updated 2.3 years ago by
GenoMax
134k • written 2.3 years ago by
mathavanbioinfo
▴ 70
3
votes
4
replies
1.0k
views
Proportion of RNAseq reads mapping to rRNA, tRNA, mRNA, and intergenic or antisense regions of the genome?
GTF
featureCounts
NGS
GFF
updated 2.3 years ago by
i.sudbery
17k • written 2.3 years ago by
mathavanbioinfo
▴ 70
0
votes
1
reply
534
views
How to view large PPI network in STRING database?
PPI
large
network
STRING
updated 2.3 years ago by
Jean-Karim Heriche
26k • written 2.3 years ago by
mathavanbioinfo
▴ 70
0
votes
3
replies
863
views
How can I get three letter organism code for cavia porcellus?
GO
three
KEGG
updated 2.4 years ago by
EagleEye
7.5k • written 2.4 years ago by
mathavanbioinfo
▴ 70
5
votes
3
replies
752
views
Where I can get the gtf file of antheraea mylitta
GTF
updated 2.4 years ago by
lieven.sterck
14k • written 2.4 years ago by
mathavanbioinfo
▴ 70
0
votes
0
replies
460
views
Extracting the genes associated drugs?
bank
Drug
2.4 years ago by
mathavanbioinfo
▴ 70
4
votes
5
replies
1.9k
views
How to download entire human protein sequences from RefSeq database hrough command line?
Refseq
programming
updated 2.5 years ago by
vkkodali_ncbi
★ 3.6k • written 2.5 years ago by
mathavanbioinfo
▴ 70
2
votes
2
replies
592
views
How to handle "perbase quality failed" issue?
RNA-Seq
fastqc
2.8 years ago by
mathavanbioinfo
▴ 70
4
votes
6
replies
2.5k
views
How to perform the lncRNA enrichment analysis?
lncRNA
enrichment
gene ontology
updated 2.8 years ago by
Qiongyi
▴ 160 • written 2.9 years ago by
mathavanbioinfo
▴ 70
2
votes
2
replies
768
views
How to identify the 300 kb upstream and downstream genes of lncRNAs?
RNA-Seq
lncRNA
target genes
upstream
downstream
updated 2.8 years ago by
JC
13k • written 2.8 years ago by
mathavanbioinfo
▴ 70
2
votes
1
reply
851
views
How to extract upstream and downstream of lncRNA in particular range?
RNA-Seq
lncRNA
hommer
bed
gtf
updated 2.8 years ago by
jordi.planells
▴ 450 • written 2.8 years ago by
mathavanbioinfo
▴ 70
1
vote
1
reply
569
views
How to find the gene name and classification using Ensembl ID?
genome
ensembl
lncRNA
updated 2.9 years ago by
Jean-Karim Heriche
26k • written 2.9 years ago by
mathavanbioinfo
▴ 70
1
vote
2
replies
997
views
How create annotation file for WGCNA for RNA-Seq data?
RNA-Seq
WGCNA
Annotaion file
updated 3.2 years ago by
Kevin Blighe
86k • written 3.2 years ago by
mathavanbioinfo
▴ 70
0
votes
1
reply
907
views
How to make annotation file for WGCNA analysis of RNA Seq data?
next-gen
updated 3.5 years ago by
Kevin Blighe
86k • written 3.5 years ago by
mathavanbioinfo
▴ 70
0
votes
2
replies
856
views
DEGS analysis with DESeq2?
DESeq2
DEGs
updated 3.5 years ago by
Biostar
20 • written 3.6 years ago by
mathavanbioinfo
▴ 70
0
votes
0
replies
777
views
lncRNA prediction using CPAT?
CPAT
lncRNA
3.5 years ago by
mathavanbioinfo
▴ 70
0
votes
1
reply
698
views
DEGs analysis with StringTie results?
StringTie
DEGs
DESeq2
3.6 years ago by
mathavanbioinfo
▴ 70
2
votes
8
replies
2.0k
views
How to get GTF file for Rousettus_aegyptiacus?
StringTie
GTF
Assembly
Rousettus aegyptiacus
3.7 years ago by
mathavanbioinfo
▴ 70
0
votes
1
reply
811
views
How to construct draft genome of virus using Trinity de novo assembler?
RNA virus
amplicons
trintiy
3.7 years ago by
mathavanbioinfo
▴ 70
0
votes
4
replies
1.7k
views
How to extract 3', 5' UTR sequences from genbank records using python, PERL and R code?
UTR
updated 3.7 years ago by
zubenel
▴ 120 • written 3.7 years ago by
mathavanbioinfo
▴ 70
0
votes
2
replies
626
views
Is virus specific UTR prediction tool available?
UTR
3.8 years ago by
mathavanbioinfo
▴ 70
0
votes
0
replies
474
views
Best assembler for WGS for RNA viruses?
WGS
3.8 years ago by
mathavanbioinfo
▴ 70
2
votes
1
reply
706
views
How to create matrix for larger data set?
matrix
RNA-Seq
updated 4.0 years ago by
ATpoint
76k • written 4.0 years ago by
mathavanbioinfo
▴ 70
0
votes
0
replies
826
views
What is the differences in index building by hisat with or without exon, splicing variant files?
lncRNA
RNA-Seq
hisat2
4.0 years ago by
mathavanbioinfo
▴ 70
0
votes
0
replies
1.4k
views
How to convert agilent probe id into gene symbol in gene expression matrix?
agilent
probe
conversion
4.0 years ago by
mathavanbioinfo
▴ 70
0
votes
0
replies
743
views
Novel lncRNA identification and quantification RNA seq?
RNA-Seq
sequencing
assembly
hisat2
lncRNA
4.0 years ago by
mathavanbioinfo
▴ 70
3
votes
21
replies
3.2k
views
Normalization agilent microarray data?
Microarray
Normalization
updated 2.4 years ago by
Ram
40k • written 4.0 years ago by
mathavanbioinfo
▴ 70
1
vote
4
replies
1.4k
views
How to extract lncRNA from CPC2 output?
RNA-Seq
Assembly
next-gen
updated 4.0 years ago by
elsoja
▴ 160 • written 4.0 years ago by
mathavanbioinfo
▴ 70
0
votes
4
replies
526
views
Is there any range for significant count of DEGs?
RNA-Seq
rna-seq
gene
4.0 years ago by
mathavanbioinfo
▴ 70
0
votes
2
replies
471
views
Where I can download index files for Rousettus aegyptiacus?
genome
rna-seq
assembly
updated 4.1 years ago by
Matteo Schiavinato
★ 3.6k • written 4.1 years ago by
mathavanbioinfo
▴ 70
0
votes
2
replies
646
views
How Interpret the hisat2 output?
ngs
updated 4.2 years ago by
Arup Ghosh
3.2k • written 4.2 years ago by
mathavanbioinfo
▴ 70
0
votes
1
reply
720
views
What is acceptable optimal overall percentage of Hisat2?
rna-seq
4.3 years ago by
mathavanbioinfo
▴ 70
0
votes
0
replies
1.2k
views
How to compare time series data of gene expression studies?
sequencing
5.7 years ago by
mathavanbioinfo
▴ 70
0
votes
1
reply
1.3k
views
microarray data analysis GEO2R results?
gene
5.9 years ago by
mathavanbioinfo
▴ 70
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