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173 results • Page
2 of 4
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1
vote
2
replies
271
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
1 day ago by
Nafi
• 0
1
vote
3
replies
257
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 2 days ago by
GenoMax
142k • written 2 days ago by
jeffrey.maurer.informatics
• 0
0
votes
2
replies
208
views
ERROR When Using Ensembl Plants Biomart Wget API
biomart
plant
ensembl
updated 2 days ago by
GenoMax
142k • written 2 days ago by
Dora
▴ 10
0
votes
0
replies
152
views
News:
Goodbye, Slow Code? How BioNumpy can Redefine Python’s Role in Bioinformatics!
BioNumPy
Python
NumPy
updated 2 days ago by
Ram
43k • written 2 days ago by
Chakri
• 0
0
votes
1
reply
168
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
updated 1 day ago by
Adam
▴ 30 • written 2 days ago by
Ahiad Chen Zion
• 0
0
votes
4
replies
254
views
Introduce SNPs on FASTA
simulation
snps
haplotypes
pharmacogenetics
updated 2 days ago by
Michael
54k • written 2 days ago by
Riccardo
▴ 10
0
votes
0
replies
121
views
barcode of TCR-sequencing
barcode
2 days ago by
yueli7
▴ 250
0
votes
0
replies
120
views
News:
Online course: Meta-analysis in R - last 2 seats left
Meta-Analysis
Statistics
R
updated 2 days ago by
Ram
43k • written 2 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
116
views
Somatic variant calling with Mutect2 using 2 matched-normals for one sample
cancer
mutect
variant-calling
GATK
somatic-variants
updated 2 days ago by
Ram
43k • written 2 days ago by
Alexandros
• 0
0
votes
1
reply
157
views
unable to get feature count results
featureCounts
updated 2 days ago by
Ram
43k • written 2 days ago by
Ravita
• 0
0
votes
3
replies
261
views
KEGG Pathways
r
RNA-seq
updated 2 days ago by
Ram
43k • written 2 days ago by
Sudip
• 0
4
votes
6
replies
3.8k
views
Taking the difference of two VCFs (or removing singletons)
genome
sequencing
singleton
SNP
filter
updated 2 days ago by
Andres
▴ 20 • written 9.6 years ago by
hermathena
▴ 40
0
votes
0
replies
123
views
Seurat object reductions (PCA, UMAP,..) after subsetting data
Seurat
2 days ago by
Bine
▴ 60
0
votes
1
reply
272
views
News:
FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last places available
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
2 days ago by
David Langenberger
11k
0
votes
0
replies
123
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
2 days ago by
8armed
• 0
0
votes
1
reply
175
views
Deseq2
Deseq2
updated 2 days ago by
Jack Tierney
▴ 360 • written 2 days ago by
Sudip
• 0
1
vote
1
reply
205
views
Polishing genome assembly
polishing
Nanopore
PacBio
updated 2 days ago by
Michael
54k • written 3 days ago by
Lissa Cruz Saavedra
• 0
5
votes
3
replies
250
views
6 follow
Integrate transcriptomic data and proteomics data.
OMICS
updated 2 days ago by
Lluís R.
★ 1.2k • written 2 days ago by
이민경[학생](대학원 융합의과학과)
• 0
2
votes
2
replies
182
views
MA plot of shrunken fold change
MA-plot
Deseq2
updated 2 days ago by
ATpoint
82k • written 2 days ago by
Sudip
• 0
1
vote
2
replies
212
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 2 days ago by
Ram
43k • written 2 days ago by
Ravita
• 0
0
votes
0
replies
106
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
2 days ago by
Adyasha
• 0
0
votes
0
replies
110
views
human gut metagenome taxonomy profile table and KO profile table from big cohort
metagenome
gut
human
2 days ago by
fanglujing
▴ 60
0
votes
0
replies
123
views
Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
2 days ago by
Jacob
• 0
0
votes
3
replies
726
views
Why cd-hit-est not work when sequence identity threshold<0.95?
genome
cluster
sequence
updated 2 days ago by
weidonglu
• 0 • written 21 months ago by
JZX
• 0
0
votes
4
replies
249
views
Perfom a Gene Ontology Analysis from GO terms txt file
RNA-Seq
GO
updated 2 days ago by
Ram
43k • written 3 days ago by
Hamtaro
▴ 50
0
votes
1
reply
174
views
Differential Accessibility
DiffBind
updated 3 days ago by
Ram
43k • written 3 days ago by
Shloka
• 0
0
votes
3
replies
264
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 2 days ago by
GenoMax
142k • written 3 days ago by
kim
• 0
3
votes
2
replies
359
views
Extract protein sequence
fasta
alignment
blast
2 days ago by
anna
▴ 20
3
votes
3
replies
307
views
Is it possible to bulk download files from GEO repository?
RNA-seq
Galaxy
Tanscriptomics
updated 3 days ago by
noodle
▴ 580 • written 3 days ago by
WUSCHEL
▴ 750
0
votes
1
reply
160
views
metagenomic virome quality assessment
viromics
metagenomics
updated 3 days ago by
Ram
43k • written 3 days ago by
Petchimuthu
• 0
3
votes
7
replies
311
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
3 days ago by
salias
• 0
0
votes
0
replies
120
views
Using limma in methylation EM-seq?
EM-seq
methylation
3 days ago by
Lluís R.
★ 1.2k
4
votes
7
replies
570
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
3 days ago by
e.r.zakiev
▴ 210
0
votes
0
replies
120
views
Synteny analysis
bacterial
synteny
genome
updated 3 days ago by
GenoMax
142k • written 3 days ago by
Namil
• 0
0
votes
4
replies
235
views
Genbank File Format
gbkformat
2 days ago by
alenew.am
• 0
0
votes
5
replies
398
views
How should I make kallisto indexes?
kallisto
updated 3 days ago by
dsull
★ 5.9k • written 17 days ago by
bioinfo
▴ 150
0
votes
0
replies
215
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma
ArrayExpress
DifferentialExpression
GEOquery
3 days ago by
SSSJec
• 0
0
votes
3
replies
205
views
Software to separate reads from different individuals
software
development
nanopore
updated 3 days ago by
GenoMax
142k • written 3 days ago by
njornet
▴ 20
0
votes
0
replies
91
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
3 days ago by
David
• 0
4
votes
5
replies
281
views
High Malat-1 expression in single cell data
cell
analysis
single
updated 3 days ago by
dsull
★ 5.9k • written 3 days ago by
Kazo
▴ 10
0
votes
2
replies
194
views
How to update R on ubuntu
installation
update
R
apt-get
3 days ago by
Bosberg
▴ 50
4
votes
0
replies
128
views
Herald:
The Biostar Herald for Monday, April 29, 2024
herald
3 days ago by
Biostar
2.7k
0
votes
1
reply
130
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
updated 3 days ago by
GenoMax
142k • written 3 days ago by
Ruqaiya
• 0
0
votes
1
reply
270
views
Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mouse Genome
breakdancer
insertion
Pindel
variation
Delly
updated 3 days ago by
trausch
★ 1.9k • written 20 days ago by
zec018
• 0
0
votes
0
replies
99
views
LEfSe
LEfSe
3 days ago by
benkosta
• 0
0
votes
0
replies
87
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq
DEXSeqDataSet
SGSeq
3 days ago by
Sara
▴ 30
1
vote
4
replies
378
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
3 days ago by
hagl
▴ 10
0
votes
4
replies
234
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
7 hours ago by
matteo.levorato
• 0
0
votes
2
replies
148
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
3 days ago by
Lluís R.
★ 1.2k
0
votes
1
reply
139
views
How to solve DESeq2 Error in checkFullRank(modelMatrix)?
RNA-Seq
DESeq2
updated 3 days ago by
i.sudbery
19k • written 3 days ago by
DOBI
• 0
173 results • Page
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Recent Votes
Answer: Interpreting TCGA .rsem.genes.results and .rsem.genes.normalized_results files.
Interpreting TCGA .rsem.genes.results and .rsem.genes.normalized_results files.
How to convert plink data from 38th assembly to 37
How to convert plink data from 38th assembly to 37
Comment: How to access TCGA samples that were treated with a specific drug?
Comment: Normalize scRNAseq data to housekeeping genes to compare several datasets
Comment: Converting CRAM to FastQ
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Recent Replies
Answer: Bedtools merge minimum overlap?
by
harold.smith.tarheel
★ 4.9k
Bedtools [intersect][1] allows you to specify the fraction of overlap between two BED (or BAM) files using the F/f/r flags. You could split…
Comment: How to access TCGA samples that were treated with a specific drug?
by
Qroid
▴ 40
Sorry, I should have been more specific. By "that list" I mean what's populated in the Therapeutic Agents tab when no filters are applied. …
Comment: Bedtools merge minimum overlap?
by
bk11
★ 2.4k
Not sure if you wanting to do like this- cat your_input.bed chr1 100 200 region1 + chr1 180 300 regi…
Comment: Extract gRNA sequence using cutadapt
by
GenoMax
142k
If you know what the boundaries of your construct look like then trim the left-end of the read using the tag on that end (`ktrim=l`). Then …
Comment: Extract gRNA sequence using cutadapt
by
gernophil
▴ 80
> Not every read in your data is going to match a guide. That is also true for sure. Let me clarify what I mean. For every read you should…
Answer: VG : No reference-sense paths available in the graph; falling back to generic pa
by
anovak
▴ 120
If your GFA has paths in it that are P lines with names that don't include a sample name, contig name, and separators, then those are what …
Comment: Extract gRNA sequence using cutadapt
by
GenoMax
142k
> if you look at a fastq file you should be able to tell for every read definitely, if it has a perfect match for a guide in it and what gu…
Answer: DiffBind: no peaks in DBA
by
jared.andrews07
★ 16k
Because `dba.analyze` is not meant to be run directly on a peaks file. Have you read the documentation? In addition, a ChIP-seq experiment…
Comment: Converting CRAM to FastQ
by
Maverick
▴ 10
Thank you so much! Will look it up right away.
Comment: Extract gRNA sequence using cutadapt
by
gernophil
▴ 80
> I don't think every guide is supposed to show up in these experiments as far as I have seen. You will get some guides with 0 counts as yo…
Comment: Converting CRAM to FastQ
by
GenoMax
142k
Use `samtools view ` for this conversion. See discussion in https://www.biostars.org/p/9592860/ Specifically @jkbonfield's comment here --…
Comment: How to access TCGA samples that were treated with a specific drug?
by
GenoMax
142k
No that was only from Breast cancer. You could try selecting all data and see if you are able to see all treatments in the set. No idea a…
Comment: Extract gRNA sequence using cutadapt
by
GenoMax
142k
I don't think every guide is supposed to show up in these experiments as far as I have seen. You will get some guides with 0 counts as you …
Comment: Extract gRNA sequence using cutadapt
by
gernophil
▴ 80
> Can you try lowering the k to k=9? Wouldn't that mess with the results since all my kmers are 20bp? > You don't have any duplicate sequ…
Comment: Provean help
by
Mensur Dlakic
★ 27k
> Else, I will happy to send over the data and kindly perform the analysis for me. This website is meant to provide advice, not service. I…
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