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184 results • Page
3 of 4
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0
votes
4
replies
263
views
Perfom a Gene Ontology Analysis from GO terms txt file
RNA-Seq
GO
updated 3 days ago by
Ram
43k • written 4 days ago by
Hamtaro
▴ 50
0
votes
1
reply
179
views
Differential Accessibility
DiffBind
updated 4 days ago by
Ram
43k • written 4 days ago by
Shloka
• 0
0
votes
3
replies
276
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 3 days ago by
GenoMax
142k • written 4 days ago by
kim
• 0
3
votes
2
replies
370
views
Extract protein sequence
fasta
alignment
blast
3 days ago by
anna
▴ 20
3
votes
3
replies
317
views
Is it possible to bulk download files from GEO repository?
RNA-seq
Galaxy
Tanscriptomics
updated 4 days ago by
noodle
▴ 580 • written 4 days ago by
WUSCHEL
▴ 750
0
votes
1
reply
166
views
metagenomic virome quality assessment
viromics
metagenomics
updated 4 days ago by
Ram
43k • written 4 days ago by
Petchimuthu
• 0
3
votes
7
replies
332
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
4 days ago by
salias
• 0
0
votes
0
replies
123
views
Using limma in methylation EM-seq?
EM-seq
methylation
4 days ago by
Lluís R.
★ 1.2k
4
votes
7
replies
578
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
4 days ago by
e.r.zakiev
▴ 210
0
votes
0
replies
124
views
Synteny analysis
bacterial
synteny
genome
updated 4 days ago by
GenoMax
142k • written 4 days ago by
Namil
• 0
0
votes
4
replies
248
views
Genbank File Format
gbkformat
3 days ago by
alenew.am
• 0
0
votes
5
replies
413
views
How should I make kallisto indexes?
kallisto
updated 4 days ago by
dsull
★ 6.0k • written 18 days ago by
bioinfo
▴ 150
0
votes
0
replies
224
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma
ArrayExpress
DifferentialExpression
GEOquery
4 days ago by
SSSJec
• 0
0
votes
3
replies
213
views
Software to separate reads from different individuals
software
development
nanopore
updated 4 days ago by
GenoMax
142k • written 4 days ago by
njornet
▴ 20
0
votes
0
replies
93
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
4 days ago by
David
• 0
0
votes
2
replies
213
views
How to update R on ubuntu
installation
update
R
apt-get
4 days ago by
Bosberg
▴ 50
4
votes
0
replies
131
views
Herald:
The Biostar Herald for Monday, April 29, 2024
herald
4 days ago by
Biostar
2.7k
1
vote
1
reply
141
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
updated 4 days ago by
GenoMax
142k • written 4 days ago by
Ruqaiya
• 0
0
votes
1
reply
274
views
Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mouse Genome
breakdancer
insertion
Pindel
variation
Delly
updated 4 days ago by
trausch
★ 1.9k • written 21 days ago by
zec018
• 0
0
votes
0
replies
105
views
LEfSe
LEfSe
4 days ago by
benkosta
• 0
0
votes
0
replies
89
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq
DEXSeqDataSet
SGSeq
4 days ago by
Sara
▴ 30
1
vote
4
replies
390
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
4 days ago by
hagl
▴ 10
0
votes
5
replies
284
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 15 hours ago by
Mohamed Abderrahmane
▴ 20 • written 4 days ago by
matteo.levorato
• 0
0
votes
2
replies
155
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
4 days ago by
Lluís R.
★ 1.2k
0
votes
1
reply
144
views
How to solve DESeq2 Error in checkFullRank(modelMatrix)?
RNA-Seq
DESeq2
updated 4 days ago by
i.sudbery
19k • written 4 days ago by
DOBI
• 0
0
votes
0
replies
99
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass
Bioinformatics
spectrometry
Proteins
4 days ago by
atharvakarkare14
▴ 30
7
votes
16
replies
708
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
4 days ago by
Ruqaiya
• 0
0
votes
2
replies
199
views
What should I consider as FASTA for dataset?
PDB
FASTA
4 days ago by
Nafi
• 0
38
votes
24
replies
1.9k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 3 days ago by
i.sudbery
19k • written 6 days ago by
noodle
▴ 580
0
votes
0
replies
215
views
Differential accessibility using DiffBinf
diffbind
4 days ago by
Shloka
• 0
0
votes
0
replies
96
views
vg call vs vg surject
vg
variation
graphs
updated 4 days ago by
GenoMax
142k • written 4 days ago by
aliraza3119
• 0
0
votes
1
reply
136
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
updated 4 days ago by
GenoMax
142k • written 4 days ago by
Winter
• 0
2
votes
7
replies
1.3k
views
6 follow
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq
Salmon
Isoseq
updated 4 days ago by
Gordon Smyth
★ 7.1k • written 8 months ago by
Calum
▴ 10
0
votes
1
reply
208
views
Finding batch and outlayers
Pca
updated 4 days ago by
christopher medway
▴ 460 • written 4 days ago by
Tigran
• 0
2
votes
2
replies
201
views
PDB related issue
rcsb
pdb
updated 4 days ago by
noodle
▴ 580 • written 5 days ago by
Nafi
• 0
0
votes
0
replies
113
views
News:
Online course: Genome Annotation
Genome-Assembly
Genome-Annotation
4 days ago by
carlopecoraro2
★ 2.5k
0
votes
8
replies
431
views
What does it mean single base resolution in sequencing?
SNP
sequencing
updated 3 days ago by
LauferVA
4.2k • written 5 days ago by
jinyu
▴ 10
0
votes
9
replies
2.5k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome
base-calling
fastq
nanopore
updated 4 days ago by
Ram
43k • written 8 months ago by
Gio
• 0
2
votes
5
replies
455
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
5 days ago by
ashaneev07
▴ 20
0
votes
1
reply
169
views
Downloading full alignments from Pfam
pfam
updated 5 days ago by
GenoMax
142k • written 5 days ago by
bef1
• 0
0
votes
1
reply
748
views
Can I run cellassign on samples independently if there is batch effect present?
RNA-Seq
R
cellassign
batch-effect
updated 5 days ago by
Francesco
▴ 10 • written 3.3 years ago by
gt
▴ 30
3
votes
2
replies
295
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 4 days ago by
i.sudbery
19k • written 7 days ago by
vanbelj
▴ 40
0
votes
0
replies
122
views
adjusting for confounders in LMER in R
confounders
LMER
R
updated 4 days ago by
dariober
14k • written 5 days ago by
rene.j.erhardt
▴ 20
1
vote
3
replies
300
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 5 days ago by
ATpoint
82k • written 6 days ago by
Francesco
▴ 10
0
votes
0
replies
139
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
6 days ago by
tnminh89
▴ 10
0
votes
0
replies
143
views
Filter low express genes in microarray data
microarray
6 days ago by
Chris
▴ 260
0
votes
1
reply
334
views
absolute path for symbolic links in Snakefile
Snakemake
updated 6 days ago by
Jesse
▴ 740 • written 14 days ago by
yifangt86
▴ 60
0
votes
2
replies
343
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment
gaps
updated 6 days ago by
Jesse
▴ 740 • written 8 days ago by
Broccoli
• 0
4
votes
3
replies
362
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 6 days ago by
Arup Ghosh
3.2k • written 7 days ago by
chaco001
▴ 40
1
vote
3
replies
387
views
Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:1.1.1.4, 1.1.1.-, 1.1.1.303)?
ontology
metagenomics
database
enzymes
genomics
updated 5 days ago by
Mensur Dlakic
★ 27k • written 6 days ago by
O.rka
▴ 710
184 results • Page
3 of 4
Recent Votes
Comment: No INFO/info value in headers
how to combine multiple RNAseq count files into a single dataframe in R and unix
Comment: Greatly speed up conda by using mamba
Greatly speed up conda by using mamba
Comment: Converting CRAM to FastQ
Parametric or non-parametric tests for qPCR significance testing between treatments?
Answer: Converting CRAM to FastQ
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142k
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Answer: visualize GSEA
by
bk11
★ 2.4k
I have made some edits in your code basically changing the position of text and commented out the line `data$text_pos <- ifelse(data$NES > …
Comment: Differential Expression Analysis using DESeq2 in R
by
swbarnes2
14k
Pictures of code are useless. You were told to paste the code and use the 0101 button. Can you explain why you decided not to do that? If…
Comment: Differential Expression Analysis using DESeq2 in R
by
Erina
• 0
![Here is the code I am using for the analysis][1] [1]: /media/images/8a511904-6ae8-47f5-b647-ee15b02b
Answer: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read
by
swbarnes2
14k
In paired end sequencing, every read has a mate, and the flags all together tell you not only what is up with the read you are looking at, …
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
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Mbofire
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Comment: Easy way to find out which allele is minor allele from bed file?
by
curious
▴ 750
According to the link: "When *generating* such filesets, PLINK 1.x defaults to swapping the alleles whenever A1's frequency is above (not …
Comment: TaxID mapping file
by
GenoMax
142k
nodesDB file should have been installed if you had used "Install" script for `blobtools` according to : https://blobtools.readme.io/docs/ta…
Comment: Parametric or non-parametric tests for qPCR significance testing between treatme
by
e.r.zakiev
▴ 210
obviously if the values are really sampled from a (quasi) normally-distributed values, then n doesn't matter, he could use t-test even with…
Comment: Converting CRAM to FastQ
by
Maverick
▴ 10
Understood Thank you!
Comment: Converting CRAM to FastQ
by
GenoMax
142k
You can use any reference that you like at this point. Since you are planning to use GATK, you can get their version from the resource bund…
Comment: Converting CRAM to FastQ
by
Maverick
▴ 10
![enter image description here][1]I was able to get my fastq files. I can see that my reference files are cached in a hts-ref directory but…
Comment: Differential Expression Analysis using DESeq2 in R
by
swbarnes2
14k
Okay, that shows us the problem, but not what we need to solve it. But, for instance, are you sure that period after the sample name shou…
Comment: Easy way to find out which allele is minor allele from bed file?
by
bk11
★ 2.4k
In the case of MAF = 0.5, I think A1 is still the minor allele. You can check the discussion in this [link][1]. [1]: https://groups.goo…
Comment: Easy way to find out which allele is minor allele from bed file?
by
curious
▴ 750
Yes, but I think the problem is what to do when MAF = 0.5
Answer: Easy way to find out which allele is minor allele from bed file?
by
bk11
★ 2.4k
In Plink, A1 is usually a minor allele and A2 a major allele. .frq (basic allele frequency report) Produced by --freq. …
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