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1,000 results • Page
1 of 20
Sort: Votes
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Votes
Replies
22
votes
20
replies
2.3k
views
what is the prefered strategy to treat with blast-less transcriptomes from RNA-seq
blast
RNA-Seq
genome
gene
updated 8 months ago by
Ram
41k • written 7.4 years ago by
Farbod
★ 3.4k
20
votes
17
replies
2.7k
views
How to add "transcript" feature to a gtf file?
gtf
updated 5 months ago by
1769mkc
★ 1.1k • written 2.8 years ago by
pomodoro_sinensis
▴ 110
18
votes
4
replies
8.5k
views
How To Find Rna-Seq Data Of Published Papers?
geo
next-gen
RNA-seq
updated 9 months ago by
Ram
41k • written 10.4 years ago by
user
▴ 940
15
votes
16
replies
1.3k
views
ncbi error report log for validate fastq issue
sra-tools
updated 10 weeks ago by
GenoMax
136k • written 10 weeks ago by
1769mkc
★ 1.1k
14
votes
18
replies
1.5k
views
Clustering in single cell
seurat
single-cell
updated 7 weeks ago by
e.r.zakiev
▴ 170 • written 10 weeks ago by
Chris
▴ 230
14
votes
5
replies
3.0k
views
bioinformatics basic training
genome
updated 9 months ago by
Ram
41k • written 9.0 years ago by
f.muoghalu
• 0
11
votes
9
replies
2.4k
views
samtools piping with awk/ bash commands -> Wonky things happen!!!
bash
samtools
awk
updated 11 months ago by
Ram
41k • written 8.5 years ago by
QVINTVS_FABIVS_MAXIMVS
★ 2.5k
10
votes
7
replies
3.5k
views
What is Pathway Analysis?
database
analysis
ontology
pathway
updated 5 months ago by
Ram
41k • written 7.7 years ago by
Pranavathiyani G
▴ 330
10
votes
15
replies
1.5k
views
Can't find a variant which suppose must have in a vcf file
variant-calling
bcftools
nf-core
5 months ago by
Chris
▴ 230
10
votes
15
replies
5.8k
views
convert fasta/gb to vcf
fasta
vcf
genbank
gff
updated 8 months ago by
Ram
41k • written 5.2 years ago by
marongiu.luigi
▴ 690
10
votes
6
replies
804
views
RNA seq, secreted protein
protein
gene
secreted
updated 4 months ago by
Joe
21k • written 12 months ago by
Rob
▴ 160
10
votes
14
replies
4.5k
views
ATAC-seq data and deepTools: Small detail with impact on output
bigwig
read-length
deeptools
ATAC-seq
updated 6 months ago by
Ram
41k • written 3.8 years ago by
gable_works
▴ 50
10
votes
6
replies
2.7k
views
which language to use for such a bioinformatics web services infrastructure?
web-services
java
updated 8 months ago by
Ram
41k • written 8.5 years ago by
lait
▴ 180
9
votes
4
replies
5.4k
views
How to analyse normalized read count?
RNA-Seq
R
updated 11 months ago by
Ram
41k • written 8.5 years ago by
pbio
▴ 150
9
votes
7
replies
1.1k
views
Reference genome location
reference
positions
FASTA
alignment
genome
updated 11 months ago by
barslmn
★ 2.0k • written 11 months ago by
Batel
• 0
9
votes
13
replies
14k
views
Sort bam file by coordinates using samtools
next-gen-sequencing
gene
rna-seq
updated 5 months ago by
Ram
41k • written 5.2 years ago by
Shahzad
▴ 30
9
votes
20
replies
3.8k
views
Solve SAM issues flagged by Picard's ValidateSamFile
Picard
SAM
updated 8 months ago by
Ram
41k • written 5.3 years ago by
marongiu.luigi
▴ 690
9
votes
16
replies
3.5k
views
6 follow
covert SAM to full length fasta
fasta
SAM
updated 8 months ago by
Ram
41k • written 5.3 years ago by
marongiu.luigi
▴ 690
9
votes
15
replies
876
views
Construction of single sequence assembly out of contigs
Contigs
Bacteria
Genome
WGS
12 days ago by
analyst
▴ 10
9
votes
4
replies
1.6k
views
On which branch in bioinformatics should a cancer researcher focus on ?
cancer
updated 8 months ago by
Ram
41k • written 7.3 years ago by
Bilal
▴ 60
9
votes
5
replies
519
views
Prophage prediction tool
prophage
PHASTER
prediction
updated 4 months ago by
GenoMax
136k • written 4 months ago by
A_heath
▴ 160
8
votes
13
replies
1.4k
views
Mapped reads not mapping to a real sequence?
bam
sam
samtools
kallisto
10 months ago by
txema.heredia
▴ 100
8
votes
5
replies
1.7k
views
BLASTp command line : filtering results by a minimum % of identity and % coverage
BLASTp
updated 11 weeks ago by
Ram
41k • written 2.2 years ago by
A_heath
▴ 160
8
votes
5
replies
3.4k
views
Is it possible to guess sequencing platform used based on a FASTQ/BAM file?
BAM
FASTQ
updated 11 months ago by
Ram
41k • written 8.5 years ago by
Andrew
▴ 60
8
votes
25
replies
2.7k
views
construction of a database
sql
noSQL
neo4j
database
updated 8 months ago by
Ram
41k • written 2.6 years ago by
Debut
▴ 20
8
votes
12
replies
3.5k
views
Use BLAST Command Line Applications to run a folder of many sequences against a database
BLAST
updated 8 months ago by
Ram
41k • written 2.3 years ago by
daver.v
▴ 30
8
votes
6
replies
620
views
How to create a Venn Diagram for overlapping SVs from a merged VCF
truvari
structural-variants
r
vcf
venn-diagram
4 weeks ago by
Matteo Ungaro
▴ 70
8
votes
7
replies
853
views
Why does Ensembl VEP provide HGVSg for some variants and not others?
vcf
VEP
6 months ago by
Jeremy Leipzig
22k
8
votes
5
replies
623
views
Frustrated with DEA results
microarray
differential-expression
updated 10 weeks ago by
dsull
★ 5.1k • written 10 weeks ago by
jopadrosa
• 0
8
votes
10
replies
1.7k
views
PyWGCNA
WGCNA
5 months ago by
yoshifumimiya
▴ 40
7
votes
7
replies
4.7k
views
RNA-Seq time series analysis using a DESeq2 spline approach yields far too many significant genes
splines
DESeq2
time-series
RNA-Seq
updated 6 months ago by
Ram
41k • written 4.9 years ago by
stu111538
▴ 80
7
votes
6
replies
1.8k
views
How to get/calculate coverage of a gene using bed file?
bed
coverage
gene
updated 8 months ago by
Ram
41k • written 2.1 years ago by
Nikhil
▴ 10
7
votes
10
replies
1.5k
views
col as names [solved]
R
updated 8 months ago by
Ram
41k • written 4.8 years ago by
demoraesdiogo2017
▴ 100
7
votes
4
replies
1.4k
views
So many Zeros (read counting)_NGS sequence analysis with R / Bioconductor: RNA-Seq workflow
alignment
RNA-Seq
R
updated 9 months ago by
Ram
41k • written 5.4 years ago by
healing80
• 0
7
votes
12
replies
1.5k
views
How to pass arguments in a bash script to perform read alignment to the reference?
exome
bwa
bash
updated 5 weeks ago by
Ram
41k • written 3.8 years ago by
Karma
▴ 310
7
votes
8
replies
3.6k
views
remove duplicated entries from BLAST result file
blast
alignment
updated 11 months ago by
Ram
41k • written 8.5 years ago by
Kumar
▴ 170
7
votes
10
replies
1.6k
views
Ubuntu 20.04 Crash
Ubuntu
updated 10 months ago by
Ram
41k • written 22 months ago by
bala
• 0
7
votes
13
replies
3.5k
views
6 follow
Is trimming necessary for RNAseq?
RNA-Seq
trimming
fastqc
updated 5 weeks ago by
ATpoint
78k • written 3.1 years ago by
Pac314
▴ 10
7
votes
8
replies
8.7k
views
Determining read count
trimmomatic
rna-seq
trinity
updated 3 months ago by
Ram
41k • written 7.6 years ago by
nikelle.petrillo
▴ 110
7
votes
12
replies
1.4k
views
Integrated genes from bulk RNA seq and ATAC seq
bulk-RNA
integrated
ATAC-seq
updated 6 months ago by
Sasha
▴ 770 • written 6 months ago by
Chris
▴ 230
7
votes
13
replies
695
views
deal with PCA and my samples
PCA
DEG
meta-analysis
5 weeks ago by
ali
• 0
7
votes
3
replies
1.4k
views
Using a Docker image with ensembl-vep
Linux
ensembl-vep
Docker
updated 12 months ago by
barslmn
★ 2.0k • written 12 months ago by
langziv
▴ 50
7
votes
8
replies
1.8k
views
How can we time a recent gene duplication event using (neutral?) DNA mutations as molecular clock?
molecular-clock
gene-duplication
phylogeny
updated 10 months ago by
Ram
41k • written 8.6 years ago by
xiaofeng.dong12
▴ 20
7
votes
4
replies
1.9k
views
useful and freely available softwares for Bioinformatics
software
updated 8 months ago by
Ram
41k • written 8.7 years ago by
Mo
▴ 920
7
votes
7
replies
1.5k
views
Nextflow rnaseq finishing early
RNA-seq
nextflow
updated 8 months ago by
Ram
41k • written 8 months ago by
Raygozak
★ 1.4k
7
votes
8
replies
3.8k
views
DEseq2 design matrix with 3 factors
RNA-seq
deseq2
updated 6 months ago by
Ram
41k • written 3.5 years ago by
kand3e
▴ 60
7
votes
6
replies
1.1k
views
On "wings" in volcano plots...
DEG
volcano
DGE
statistics
DE
updated 6 months ago by
ATpoint
78k • written 6 months ago by
kalavattam
▴ 190
7
votes
4
replies
1.5k
views
microarray gene datasets
gene
updated 10 months ago by
Ram
41k • written 8.6 years ago by
bioinfo
▴ 60
7
votes
2
replies
3.3k
views
Counting reads for gene transcripts with overlapping loci
RNA-Seq
gene
R
updated 11 months ago by
Ram
41k • written 8.5 years ago by
Ruet
▴ 70
7
votes
16
replies
2.5k
views
Insert size selection for RNASeq data: does it make sense?
RNA-Seq
sequencing
updated 8 months ago by
Ram
41k • written 6.2 years ago by
Matteo Schiavinato
★ 3.6k
1,000 results • Page
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Recent Votes
Answer: Renaming fasta files with their headers
Answer: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 202
Answer: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 202
Comment: Renaming fasta files with their headers
Comment: What apps can read large FASTQ files on Windows?
Answer: What are the methods to correlate/study metabolomics data to proteomics data?
Answer: What are the methods to correlate/study metabolomics data to proteomics data?
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Recent Replies
Answer: Renaming fasta files with their headers
by
shenwei356
8.3k
I've got a general method, but you need to have some basic knowledge of regular expressions. If not, please learn them for 30 minutes: -…
Comment: Renaming fasta files with their headers
by
liorglic
★ 1.3k
It's hard to understand what your input and desired output look like. Please edit your original question so it includes a clear explanation…
Comment: SRA toolkit (NCBI) - sra to fasta
by
ATpoint
78k
Can be 23 or 109, it does not matter.
Comment: Renaming fasta files with their headers
by
sebabiokr
▴ 10
Thank you for your code, but i have a fasta file which contains [gene=rps12] ids, so i want to rename the header with gene id alone like >r…
Answer: How to speed-up to contruct phylogenetic tree
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Mensur Dlakic
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It depends on how long your protein is. Generally speaking, it shouldn't take weeks or months. Trees with more than ~100 branches are very …
Comment: How to speed-up to contruct phylogenetic tree
by
liorglic
★ 1.3k
Is there a specific reason you need to use MEGA? Maybe try another software which might be faster (e.g. PhyML, RaxML, IQ-TREE). Also, do yo…
Answer: Renaming fasta files with their headers
by
liorglic
★ 1.3k
Assuming that you have a directory containing multiple files with `.fasta` extension, each containing one record, you can do something like…
Comment: What are the methods to correlate/study metabolomics data to proteomics data?
by
LauferVA
3.8k
thank you, @wuschel, for the comprehensive reply.
Comment: Renaming fasta files with their headers
by
sebabiokr
▴ 10
i tried this command awk -F 'gene=|]|[.]{1}' '/^>/ {print $2}' 7seqNC_018552.1cds.fasta > 7NC_018552.fasta got only gene name alone wit…
Answer: Converting a .frq file to a data frame?
by
zau saa
▴ 70
simply add a word to line 1 as the name of column 6
Comment: SRA toolkit (NCBI) - sra to fasta
by
Sanjukta
• 0
Hi there, will it be an issue if we do not mention 60?
Comment: Renaming fasta files with their headers
by
sebabiokr
▴ 10
Yes there are many answer in this forum but they are specific to header line. it doesnot work with my header line and its difficult for me …
Answer: What are the methods to correlate/study metabolomics data to proteomics data?
by
WUSCHEL
▴ 740
There are various methods to correlate and study metabolomics data to proteomics data. These methods can be broadly categorized into: 1. C…
Comment: Renaming fasta files with their headers
by
Mensur Dlakic
★ 25k
This type of question is among the most frequently asked on this forum. Searching through previous posts should give you several different …
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LauferVA
3.8k
they are still actively developing it. it will continue to get some of the functionality that gpt3.5 has over time. val
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