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186 results • Page
3 of 4
Sort: replies
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Votes
Replies
0
votes
1
reply
578
views
Basic stats in hierfstat
Fst
stats
hierfstat
updated 2 days ago by
mdav
• 0 • written 18 months ago by
Zoe
• 0
0
votes
1
reply
266
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
updated 2 days ago by
Scooter
▴ 280 • written 8 days ago by
avocado123
• 0
0
votes
1
reply
82
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 4 hours ago by
GenoMax
142k • written 11 hours ago by
Ximena
• 0
0
votes
1
reply
216
views
Subsetting and merging back Seurat Object brings different results
Seurat
1 day ago by
Bine
▴ 60
0
votes
1
reply
277
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
3 days ago by
David Langenberger
11k
0
votes
1
reply
182
views
Deseq2
Deseq2
updated 3 days ago by
Jack Tierney
▴ 360 • written 4 days ago by
Sudip
• 0
1
vote
1
reply
218
views
Polishing genome assembly
polishing
Nanopore
PacBio
updated 3 days ago by
Michael
54k • written 4 days ago by
Lissa Cruz Saavedra
• 0
1
vote
1
reply
154
views
Super ehancers
enhancers
updated 1 day ago by
jared.andrews07
★ 16k • written 1 day ago by
Oburah
• 0
1
vote
1
reply
132
views
Discrepancy in read counts from fastq
downsampling
fastq
updated 1 day ago by
Ram
43k • written 1 day ago by
marco.barr
▴ 90
0
votes
1
reply
773
views
cnetplot category names are too long
clusterprofiler
RNA-Seq
enrichplot
cnetplot
updated 1 day ago by
Ram
43k • written 2.7 years ago by
carov
• 0
0
votes
1
reply
492
views
Loss of 'var' using concatenation of AnnData objects
Scanpy
AnnData
updated 1 day ago by
Hugo
• 0 • written 4 months ago by
Rachel
• 0
0
votes
1
reply
54
views
HCL database download
database
HCL
human
updated 4 hours ago by
GenoMax
142k • written 5 hours ago by
sooni
▴ 20
0
votes
1
reply
133
views
Provean help
variant
Provean
updated 1 day ago by
Mensur Dlakic
★ 27k • written 1 day ago by
Arun Sai Kumar
• 0
0
votes
1
reply
180
views
Differential Accessibility
DiffBind
updated 4 days ago by
Ram
43k • written 4 days ago by
Shloka
• 0
0
votes
1
reply
135
views
VG : No reference-sense paths available in the graph; falling back to generic paths.
vg
updated 1 day ago by
anovak
▴ 120 • written 1 day ago by
Hang
• 0
0
votes
1
reply
167
views
metagenomic virome quality assessment
viromics
metagenomics
updated 4 days ago by
Ram
43k • written 4 days ago by
Petchimuthu
• 0
0
votes
1
reply
174
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core
16S
amplicon
dada2
ampliseq
updated 1 day ago by
Chris Dean
▴ 390 • written 1 day ago by
sovrappensiero
▴ 90
0
votes
1
reply
335
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
1
reply
542
views
HOMER on AWS
HOMER
updated 1 day ago by
clairechung112
• 0 • written 2.2 years ago by
Bogdan
★ 1.4k
0
votes
1
reply
137
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
updated 4 days ago by
GenoMax
142k • written 5 days ago by
Winter
• 0
1
vote
1
reply
99
views
DSEQ2 analysis
DSEQ2
logfoldchane
updated 22 hours ago by
ATpoint
82k • written 22 hours ago by
adi.gershon1
• 0
1
vote
1
reply
143
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
updated 4 days ago by
GenoMax
142k • written 5 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
1
reply
47
views
Segmentation error while using a tool
smalt
updated 30 minutes ago by
Thanujay S
• 0 • written 3 hours ago by
Ruqaiya
• 0
0
votes
1
reply
85
views
Design matrix Differential expression analysis
RNA-seq
Differential-expression
updated 1 hour ago by
Ram
43k • written 10 hours ago by
SHN
▴ 40
0
votes
1
reply
210
views
Finding batch and outlayers
Pca
updated 4 days ago by
christopher medway
▴ 460 • written 5 days ago by
Tigran
• 0
0
votes
1
reply
145
views
How to solve DESeq2 Error in checkFullRank(modelMatrix)?
RNA-Seq
DESeq2
updated 4 days ago by
i.sudbery
19k • written 5 days ago by
DOBI
• 0
0
votes
1
reply
79
views
filtering before dada2
bbduk
qiime2
dada2
metagenomic
updated 1 hour ago by
Ram
43k • written 11 hours ago by
Valentina
• 0
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
68
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 1 hour ago by
Thanujay S
• 0 • written 16 hours ago by
yahn
• 0
0
votes
1
reply
89
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
updated 13 hours ago by
GenoMax
142k • written 14 hours ago by
Lada
▴ 30
0
votes
1
reply
750
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
0
votes
1
reply
88
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
updated 12 hours ago by
swbarnes2
14k • written 12 hours ago by
kalavattam
▴ 190
0
votes
1
reply
96
views
visualize GSEA
enrichment
barplot
RNA-seq
GSEA
positive
updated 10 hours ago by
bk11
★ 2.4k • written 12 hours ago by
Rob
▴ 170
0
votes
1
reply
165
views
unable to get feature count results
featureCounts
updated 3 days ago by
Ram
43k • written 3 days ago by
Ravita
• 0
1
vote
1
reply
170
views
Including plasmid in alignment
Bacteria
Transcriptomics
BOWTIE2
STAR
3 days ago by
heelpPlease
• 0
1
vote
1
reply
224
views
Adjust pvalue in R with different approach give me all different outcome
statistics
R
p-value
updated 3 days ago by
Ram
43k • written 3 days ago by
Jonathan Yoou
▴ 60
0
votes
1
reply
563
views
after selecting specific GO terms to plot, cneplot is not showing any color for genes, GO terms and only showing lines without nodes.
cneplot
updated 3 days ago by
Ram
43k • written 3 days ago by
Dr Huma Naz
• 0
0
votes
1
reply
172
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
updated 7 hours ago by
chrchang523
10k • written 3 days ago by
8armed
• 0
0
votes
1
reply
177
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated 2 days ago by
i.sudbery
19k • written 3 days ago by
Edmond
• 0
1
vote
1
reply
959
views
News:
The GDC Legacy Archive is retiring soon.
genomic-data-commons
tcga
gdc
updated 6 hours ago by
lcordeiro
▴ 40 • written 14 months ago by
Zhenyu Zhang
★ 1.2k
0
votes
1
reply
212
views
How to find overlap of clusters in two seurat porject
clustering
seurat
updated 2 days ago by
Adam
▴ 30 • written 3 days ago by
J
• 0
0
votes
0
replies
125
views
News:
Online course: Meta-analysis in R - last 2 seats left
Meta-Analysis
Statistics
R
updated 3 days ago by
Ram
43k • written 3 days ago by
carlopecoraro2
★ 2.5k
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
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
4
votes
0
replies
131
views
Herald:
The Biostar Herald for Monday, April 29, 2024
herald
4 days ago by
Biostar
2.7k
0
votes
0
replies
129
views
Seurat object reductions (PCA, UMAP,..) after subsetting data
Seurat
3 days ago by
Bine
▴ 60
0
votes
0
replies
93
views
Tassel 5 GBS: GBSSeqToTagDBPlugin producing empty database
GBS
Tassel5
2 days ago by
meck
• 0
0
votes
0
replies
118
views
Looking for the best way to interpret these data
RNA-seq
ontology
GO
updated 2 days ago by
Ram
43k • written 2 days ago by
Oscar
▴ 10
0
votes
0
replies
65
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
15 hours ago by
Javier
• 0
186 results • Page
3 of 4
Recent Votes
Comment: Help with choosing a model species for Augustus for a de novo assembled genome.
A: After read mapping, count exons or genes?
After read mapping, count exons or genes?
Merging a large number of VCF files
A: Merging a large number of VCF files
A: pulling snps from vcf file using ids
pulling snps from vcf file using ids
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Recent Replies
Comment: Segmentation error while using a tool
by
Thanujay S
• 0
Hey @Ruqaiya! Can you please give more details on why smalt is opted here? According to what I can see, the tool has become obsolete! Why …
Comment: Extracting mutation status from MAF files - TCGA
by
Thanujay S
• 0
Hey! Can you explain the question further? What have you tried?
Comment: Downloading older version of a tool
by
Ruqaiya
• 0
I tried the 2nd option only. I got the files of older version from the author but that version isn't working on my WSL, it's showing Segmen…
Comment: filtering before dada2
by
GenoMax
142k
> I encountered a significant decrease in the percentage of merged reads. You can check with `bbmerge.sh` from BBMap suite to see how many…
Comment: HCL database download
by
GenoMax
142k
Isn't the download link available above the plot: http://bis.zju.edu.cn/HCL/data/DGE/Adult-Transverse-Colon1_dge.txt.gz
Comment: fastq screen aligner no specified.
by
GenoMax
142k
You need to change this configuration file to point it to the location where the aligner executable can be found. So as an example followi…
Answer: Design matrix Differential expression analysis
by
Gordon Smyth
★ 7.1k
The expression levels do not change but the way that you have parametrized the expression levels does change. The two design matrices give…
Comment: The GDC Legacy Archive is retiring soon.
by
lcordeiro
▴ 40
Hi Zhenyu, do you happen to know how I can download metadata for some of the legacy files? I downloaded several IDATs from the legacy data …
Answer: Force PLINK2 to neglect chrX as the sex chromosome
by
chrchang523
10k
(cross-posted from https://groups.google.com/g/plink2-users/c/Qphx_6BpPII ) You need to use --chr-set, not --allow-extra-chr, to specify…
Answer: Easy way to find out which allele is minor allele from bed file?
by
chrchang523
10k
This question does not make sense. If you care about allele-order "information [being] lost in downstream applications", REF/ALT is the ob…
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
by
Mbofire
• 0
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