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1,000 results • Page
1 of 20
Sort: Rank
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Views
Votes
Replies
0
votes
0
replies
8
views
How to cluster .faa files?
faa
protein
clustering
amino-acids
16 minutes ago by
bioinformagician
• 0
2
votes
3
replies
63
views
How to speed-up to contruct phylogenetic tree
MEGA
tree
phylogenetic
updated 20 minutes ago by
Michael
53k • written 2 hours ago by
Nelo
▴ 20
0
votes
0
replies
13
views
i ues schicexplorer's hicbuildmatrix code complains that two sam files do not have the same reads order
hicbuidmatrix
schic
39 minutes ago by
1125195245
• 0
3
votes
8
replies
174
views
Renaming fasta files with their headers
Linux
fasta
commands
52 minutes ago by
sebabiokr
▴ 10
0
votes
0
replies
33
views
PacBio subreads.fastq files?
subreads.fastq
ncbi
PacBbio
3 hours ago by
majeedaasim
▴ 60
1
vote
2
replies
87
views
Converting a .frq file to a data frame?
R
.frq
MAF
updated 10 minutes ago by
colindaven
5.8k • written 7 hours ago by
arnold
• 0
773
votes
164
replies
129k
views
107 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 9 weeks ago by
Biostar
2.3k • written 7.0 years ago by
Istvan Albert
99k
3
votes
2
replies
223
views
What are the methods to correlate/study metabolomics data to proteomics data?
metabolomics
proteomics
multiomics
updated 2 hours ago by
LauferVA
3.8k • written 18 days ago by
WUSCHEL
▴ 740
0
votes
0
replies
53
views
Loss of 'var' using concatenation of AnnData objects
var
Scanpy
AnnData
Concatenation
9 hours ago by
Rachel
• 0
0
votes
0
replies
62
views
Is there any s/w that can be used to map metabolite results to it's pathway/s?
R
metabolomics
proteomics
Python
11 hours ago by
WUSCHEL
▴ 740
0
votes
1
reply
191
views
Cibersort input data
cibersort
updated 18 hours ago by
Kaia
• 0 • written 2 days ago by
Maryam
• 0
1
vote
1
reply
144
views
What's the acceptable threshold in Quality Assessment for Genome Assemblies?
control
genome
QUAST
quality
assembly
kbase
updated 22 hours ago by
liorglic
★ 1.3k • written 1 day ago by
JaneZheng0406
• 0
0
votes
1
reply
227
views
Tutorials for Spatial Transcriptomics
ST-Seq
Scanpy
Seurat
updated 1 day ago by
CTLong
▴ 50 • written 2 days ago by
saqlain
▴ 90
3
votes
4
replies
284
views
What apps can read large FASTQ files on Windows?
fastq
apps
updated 1 hour ago by
ATpoint
78k • written 1 day ago by
Sanjukta
• 0
0
votes
0
replies
90
views
Tutorial:
download metadata using GEOquery
biology
GEO
metadata
computational
1 day ago by
Ming Tommy Tang
★ 3.6k
0
votes
0
replies
86
views
Using Metagenome Samples for HNSCC analysis
Linux
DESEQ2
SRA
Bioinformatics
ComputationalBiology
1 day ago by
Ozymandeus
▴ 30
1
vote
2
replies
238
views
Bowtie 2 alignment
Bowtie2
updated 2 days ago by
Istvan Albert
99k • written 2 days ago by
Elizabeth
▴ 30
2
votes
6
replies
415
views
which statistical test and which package for comapre datasets?
R
package
statistical
test
updated 4 hours ago by
LauferVA
3.8k • written 1 day ago by
satva72
• 0
0
votes
3
replies
247
views
Is interleaved Fastq files the same as interlaced fastq
manipulation
Data
updated 1 day ago by
GenoMax
136k • written 1 day ago by
RCMC
• 0
10
votes
6
replies
4.9k
views
How to create interval list from reference fasta or dict file?
GATK
updated 1 day ago by
Manuel Sokolov Ravasqueira
▴ 100 • written 2.9 years ago by
MatthewP
★ 1.3k
0
votes
5
replies
299
views
GetPileupSummaries intervals-list with Targeted Sequencing?
Variant-Calling
Somatic
intervals.bed
GetPileUpSummaries
GATK
updated 1 day ago by
Pierre Lindenbaum
158k • written 1 day ago by
Manuel Sokolov Ravasqueira
▴ 100
0
votes
0
replies
107
views
Test for multiplicative effect in mendelian randomization?
R
mendelian_randomization
GWAS
1 day ago by
clairvoyant
• 0
0
votes
1
reply
176
views
Is GeSeq currently unavailable?
GeSeq
updated 2 days ago by
GenoMax
136k • written 2 days ago by
zy
• 0
0
votes
4
replies
424
views
using RSEM with non Trinity assembly
SPAdes
Trinity
RSEM
updated 6 days ago by
Dunois
★ 2.4k • written 13 days ago by
jen
• 0
0
votes
1
reply
974
views
How to run Aracne cytoscape plugin ?
R
software error
rna-seq
updated 2 days ago by
gentlemonster
• 0 • written 3.2 years ago by
prithvi.mastermind
▴ 50
0
votes
2
replies
237
views
autodock vina on mac
docking
mgltools
virtualbox
1 day ago by
iamsmor
• 0
0
votes
1
reply
193
views
How can I obtain the DNA sequences of each CDS for several genbank files?
genbank
DNA
sequence
updated 2 days ago by
Ram
41k • written 2 days ago by
Raphaëlle
• 0
0
votes
1
reply
185
views
identifying SNPs from short read sequencing data
Sequencing
updated 2 days ago by
GenoMax
136k • written 2 days ago by
reaset41
• 0
0
votes
0
replies
492
views
Transcript Assembly for Multiple Species Using StringTie and Orthogroup Discovery using OrthoFinder
Species
StringTie
Orthogroups
Transcript
Assembly
2 days ago by
dtnondorf
• 0
0
votes
1
reply
186
views
Java class error message when using BBDuk
rna-seq
bbduk
updated 2 days ago by
GenoMax
136k • written 2 days ago by
milewski
• 0
0
votes
0
replies
136
views
how to run the compare_genomes for comparative analysis
genome
orthofinder
evolution
2 days ago by
rj.rezwan
• 0
2
votes
8
replies
2.0k
views
7 follow
LCA from BLAST output
lca
blast
updated 1 day ago by
Dunois
★ 2.4k • written 3.1 years ago by
makrez
▴ 50
0
votes
0
replies
136
views
Infer ancestry for RNA-seq data
plink
admixture
ancestry
updated 2 days ago by
Ram
41k • written 2 days ago by
Matthew Chang
• 0
1
vote
3
replies
264
views
CIGAR and query sequence lengths differ
pysam
samtools
2 days ago by
ManuelDB
▴ 80
1
vote
3
replies
237
views
GO, KEGG, GSEA analysis with ~5 DEGs
GO
KEGG
updated 2 days ago by
Istvan Albert
99k • written 2 days ago by
foejvs546
▴ 10
5
votes
3
replies
286
views
Rstudio cloud
R
single-cell
2 days ago by
synat.keam
▴ 80
0
votes
0
replies
128
views
Apply BSQR for Targeted Sequencing
GenomicPipelines
GATK
variant-calling
2 days ago by
Manuel Sokolov Ravasqueira
▴ 100
0
votes
1
reply
192
views
WGCNA Dendrogram Branch missing from modules
WGCNA
dendrogram
hdWGCNA
updated 1 day ago by
andres.firrincieli
3.5k • written 2 days ago by
mhale
• 0
0
votes
0
replies
125
views
bcftools=1.18 not filtering correcting MAF
bcftools
minor-allele-frequency
VCF
updated 2 days ago by
Ram
41k • written 2 days ago by
AMARU
• 0
1
vote
1
reply
183
views
How to subtract variants from one VCF file to another?
joint-genotyping
vcf
variant-calling
gatk
updated 2 days ago by
Pierre Lindenbaum
158k • written 2 days ago by
cee28
▴ 30
0
votes
2
replies
236
views
Alternative to Gentrome?
salmon
updated 11 hours ago by
cfos4698
▴ 920 • written 2 days ago by
yee
• 0
0
votes
0
replies
128
views
Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
Gene-Expression
DESeq2
updated 2 days ago by
Ram
41k • written 2 days ago by
aehall26
• 0
18
votes
4
replies
515
views
6 follow
Forum:
What Are The Most Influential Bioinformatics/Computational Biology Papers Of 2023?
genomics
snps
survey
papers
updated 2 days ago by
Ram
41k • written 2 days ago by
Raony Guimarães
★ 1.4k
0
votes
0
replies
133
views
Finding differentially expressed genes between Seurat clusters
Seurat
updated 2 days ago by
Ram
41k • written 2 days ago by
Bine
▴ 50
0
votes
0
replies
131
views
JoinLayers function for Seurat Object for annotation with SingleR
Seurat
updated 2 days ago by
Ram
41k • written 2 days ago by
Bine
▴ 50
0
votes
0
replies
144
views
Error: Failed to open /ROH/.log. Try changing the --out parameter.
plink
ROH
2 days ago by
sevda
• 0
1
vote
5
replies
298
views
Normalization of RNA captureSeq data (<20 genes captured)
captureSeq
edgeR
DESeq2
RNA
ERCC
updated 2 days ago by
ATpoint
78k • written 2 days ago by
jips
• 0
1
vote
1
reply
209
views
How to properly mock a (Pysam) read
pysam
updated 2 days ago by
Istvan Albert
99k • written 3 days ago by
ManuelDB
▴ 80
9
votes
15
replies
7.4k
views
Efficient way of calculating the number of mismatches between two sets of sequences please?
alignment
genome
sequence
updated 21 months ago by
Ram
41k • written 9.0 years ago by
Aurelie MLB
▴ 360
3
votes
3
replies
310
views
How to avoid missannotated GO terms?
swissprot
GO
enrichment
updated 3 days ago by
Elisabeth Gasteiger
★ 2.3k • written 3 days ago by
Dr.Animo
▴ 80
1,000 results • Page
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Recent Votes
Answer: Converting a .frq file to a data frame?
Answer: Multi-factor designs in DiffBind
Answer: How to speed-up to contruct phylogenetic tree
Comment: How to speed-up to contruct phylogenetic tree
Answer: Renaming fasta files with their headers
Comment: What apps can read large FASTQ files on Windows?
Answer: Renaming fasta files with their headers
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Recent Replies
Comment: Converting a .frq file to a data frame?
by
colindaven
5.8k
Also get rid of the curly braces in the col5 header `{}`
Answer: How to speed-up to contruct phylogenetic tree
by
Michael
53k
I agree with the other recommendations and I wouldn't recommend MEGA either, but would like to add that most programs, including MEGA, have…
Comment: Renaming fasta files with their headers
by
sebabiokr
▴ 10
Yes, Its perfectly working.. It will be useful if you share concat command too if there are same genes in the fasta file Thank you
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
by
Mensur Dlakic
★ 25k
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
▴ 80
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 …
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