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1,000 results • Page
1 of 20
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Votes
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0
votes
0
replies
8
views
i ues schicexplorer's hicbuildmatrix code complains that two sam files do not have the same reads order
hicbuidmatrix
schic
11 minutes ago by
1125195245
• 0
0
votes
0
replies
32
views
PacBio subreads.fastq files?
subreads.fastq
ncbi
PacBbio
2 hours ago by
majeedaasim
▴ 60
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
10 hours ago by
WUSCHEL
▴ 740
0
votes
0
replies
86
views
Using Metagenome Samples for HNSCC analysis
Linux
DESEQ2
SRA
Bioinformatics
ComputationalBiology
1 day ago by
Ozymandeus
▴ 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
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
106
views
Test for multiplicative effect in mendelian randomization?
R
mendelian_randomization
GWAS
1 day ago by
clairvoyant
• 0
0
votes
1
reply
175
views
Is GeSeq currently unavailable?
GeSeq
updated 2 days ago by
GenoMax
136k • written 2 days ago by
zy
• 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
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
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
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
124
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
0
votes
2
replies
235
views
Alternative to Gentrome?
salmon
updated 10 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
0
votes
0
replies
132
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
130
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 2 days ago by
ManuelDB
▴ 80
1
vote
2
replies
247
views
Where to download excel file to include major human disease, prevalence and incidence?
Disease
Burden
updated 3 days ago by
GenoMax
136k • written 3 days ago by
Shicheng Guo
★ 9.3k
0
votes
0
replies
143
views
how to label Histological regions on the H&E images in 10x visium H&E images
spatial-transcriptome
updated 2 days ago by
Ram
41k • written 3 days ago by
naodaigua_weng
• 0
0
votes
0
replies
149
views
Converting txt.gz to PLINK bim
S-LDSC
file
LDSC
format
3 days ago by
X
• 0
0
votes
3
replies
239
views
Convert NCBI Downloaded files to ANNOVAR format
ANNOVAR
updated 3 days ago by
Ram
41k • written 3 days ago by
robert
• 0
0
votes
0
replies
123
views
Confusing results from FindConservedMarkers in Seurat
10XGenomics
3 days ago by
pm2012
▴ 140
0
votes
5
replies
318
views
Differential expression using Bowtie2
Transcriptome
Bowtie
Differential-expression
updated 2 days ago by
ATpoint
78k • written 3 days ago by
8d8fc19e
• 0
0
votes
0
replies
109
views
use GEOparse to download series supplemental files?
gse
geoparse
python
geoquery
geo
3 days ago by
mk
▴ 290
0
votes
2
replies
206
views
How to perform quality control for sex when there are no variants after thresholding for MAF
sex
check
genetics
3 days ago by
kl
▴ 10
1
vote
2
replies
197
views
recommend gene ranking methods when doing GSEA
Gene_rank
GSEA
2 days ago by
luckyday1661
• 0
0
votes
3
replies
227
views
Opinion on miRNA pipeline
miRNA
pipeline
updated 2 days ago by
Barry Digby
★ 1.3k • written 3 days ago by
ju_ra
• 0
0
votes
1
reply
124
views
Does orthofinder allow more than one proteome per species as input ?
comparative-genomics
orthology
updated 3 days ago by
Ram
41k • written 3 days ago by
Sara
• 0
1
vote
4
replies
212
views
select unique samples in R
statistics
r
biostatistics
updated 3 days ago by
bk11
★ 1.8k • written 3 days ago by
Bioinfonext
▴ 440
0
votes
0
replies
95
views
how to run GSEA with spesific background
RNA-seq
GSEA
updated 3 days ago by
Ram
41k • written 3 days ago by
Chava
• 0
0
votes
0
replies
100
views
inverse normal p-value combination results giving NaN.
inverse
meta-Analysis
p-value
rnaseq
normal
3 days ago by
sehriban.buyukkilic
• 0
0
votes
1
reply
167
views
scRNA data analysis , how to compare pattern in multiple samples
R
scRNA
updated 3 days ago by
Ram
41k • written 4 days ago by
Confused_human
▴ 20
0
votes
1
reply
161
views
absolute running error: Error in if (!is.na(res)) { : the condition has length > 1
ABSOLUTE
error
4 days ago by
qiuting
• 0
0
votes
0
replies
107
views
cosinoRmixedeffect: an R package for mixed-effects cosinor models
interactionmodel
cosinor
mixedeffect
circadian
4 days ago by
Agnia
• 0
2
votes
3
replies
252
views
Annotation Visualization IGV
igv
alignment
gff
annotation
visualization
updated 4 days ago by
Pierre Lindenbaum
158k • written 4 days ago by
awhale01
• 0
0
votes
3
replies
255
views
Curated model organism gene functional annotations
Interpro
C.elegans
GO-terms
updated 3 days ago by
manaswwm
▴ 490 • written 4 days ago by
ian.will
▴ 10
2
votes
4
replies
381
views
An issue with gtf file (ballgownrsem)
Ballgown
RNA-seq
GTF
RSEM
4 days ago by
cucindarko51
• 0
0
votes
2
replies
220
views
Very low successfully assigned alignments with feature counts
featureCounts
RNA-seq
updated 4 days ago by
Istvan Albert
99k • written 4 days ago by
Manuel
• 0
0
votes
0
replies
116
views
ASEReadCounter output wrong number of coverage
ASEReadCounter
5 days ago by
junhuili
• 0
1
vote
1
reply
1.3k
views
How to interpret the discrepancy of assignment rate in featurecounts using forward and reverse strand protocols
RNAseq
updated 5 days ago by
charles.feigin
• 0 • written 7 weeks ago by
xinrantian
▴ 20
0
votes
0
replies
105
views
megablast taxonomy assign in blobtools
blobtools
5 days ago by
bs
• 0
1,000 results • Page
1 of 20
Recent Votes
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
Answer: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 202
Answer: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 202
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Recent Replies
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
▴ 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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