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46 results • Page
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16
votes
12
replies
7.3k
views
10 follow
how to split multi-fasta file into single fasta file named by header
genome
perl
python3
bash
python
updated 22 hours ago by
rsieber
▴ 10 • written 3.1 years ago by
Kumar
▴ 120
9
votes
9
replies
467
views
High Malat-1 expression in single cell data
cell
analysis
single
updated 15 hours ago by
dsull
★ 6.0k • written 4 days ago by
carolofharvest
▴ 30
5
votes
5
replies
541
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 12 hours ago by
Mbofire
• 0 • written 9 days ago by
Ming Tommy Tang
★ 3.9k
4
votes
15
replies
1.6k
views
how to test for differential expression in samples where a global increase in gene expression is expected
edgeR
DESeq
Differential-Expression
RNA-Seq
updated 3 hours ago by
Gordon Smyth
★ 7.1k • written 4 months ago by
raplayer
▴ 10
4
votes
9
replies
2.1k
views
6 follow
Same sequencing sample in multiple lanes. How to analyse it?
sequencing
bowtie2
alignment
samtools
ngs
updated 16 hours ago by
ST
• 0 • written 2.2 years ago by
Federico
• 0
3
votes
5
replies
195
views
Generating mpileup file using samtools
mpileup
samtools
updated 19 hours ago by
Joe
21k • written 22 hours ago by
Ruqaiya
• 0
3
votes
3
replies
292
views
What analysis suitable to identify similarly expressed genes between two samples (treated vs untreated). Contrary to DGE analysis,
Gene-Expression
RNA
NOISeq
DGE
updated 21 hours ago by
ATpoint
82k • written 1 day ago by
alifafiq1
• 0
3
votes
5
replies
248
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
13 hours ago by
Maverick
▴ 10
2
votes
2
replies
143
views
Analysis of intronic reads included scRNA-seq data
cell
single
updated 18 hours ago by
t.montserrat.ayuso
▴ 10 • written 21 hours ago by
carolofharvest
▴ 30
2
votes
3
replies
195
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 16 hours ago by
dthorbur
★ 1.9k • written 1 day ago by
Vijith
▴ 30
2
votes
2
replies
1.8k
views
Parametric or non-parametric tests for qPCR significance testing between treatments?
qPCR
statistical test
parametric
non-parametric
updated 13 hours ago by
e.r.zakiev
▴ 210 • written 3.8 years ago by
n.anuragsharma
▴ 40
1
vote
2
replies
277
views
read length in structural variant calling
nanopore
SV
QC
ONT
variant
20 hours ago by
eebloom
▴ 80
1
vote
2
replies
198
views
RNA-seq data for deep learning classification
rna-seq
19 hours ago by
yahn
• 0
1
vote
5
replies
309
views
Introduce SNPs on FASTA
simulation
snps
haplotypes
pharmacogenetics
22 hours ago by
Riccardo
▴ 10
1
vote
3
replies
213
views
Odd alignment question/finding
Alignment
updated 21 hours ago by
barslmn
★ 2.1k • written 2 days ago by
poordumbsillyidiot
• 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
1
vote
1
reply
98
views
DSEQ2 analysis
DSEQ2
logfoldchane
updated 21 hours ago by
ATpoint
82k • written 21 hours ago by
adi.gershon1
• 0
1
vote
6
replies
328
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 15 hours ago by
GenoMax
142k • written 18 days ago by
eebloom
▴ 80
1
vote
3
replies
210
views
Does comparing two different groups to a common third group introduce bias in the analysis?
DESEQ
RNAseq
updated 23 hours ago by
ATpoint
82k • written 1 day ago by
Qi
• 0
1
vote
7
replies
422
views
Downsampling long-read BAM files
nanopore
BAM
QC
ONT
downsampling
20 hours ago by
eebloom
▴ 80
0
votes
2
replies
129
views
Downloading older version of a tool
Alignment
tools
3 hours ago by
Ruqaiya
• 0
0
votes
1
reply
84
views
Design matrix Differential expression analysis
RNA-seq
Differential-expression
updated 1 hour ago by
Ram
43k • written 9 hours ago by
SHN
▴ 40
0
votes
0
replies
58
views
Quetion regarding WGCNA
WGCNA
Network-construction
updated 1 hour ago by
Ram
43k • written 9 hours ago by
deepak180001
• 0
0
votes
1
reply
78
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
64
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 48 minutes ago by
Thanujay S
• 0 • written 15 hours ago by
yahn
• 0
0
votes
5
replies
288
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 23 hours ago by
Mohamed Abderrahmane
▴ 20 • written 4 days ago by
matteo.levorato
• 0
0
votes
1
reply
40
views
Segmentation error while using a tool
smalt
updated 10 minutes ago by
Thanujay S
• 0 • written 3 hours ago by
Ruqaiya
• 0
0
votes
5
replies
255
views
6 follow
What purposes can TPM values be used for?
RNA-seq
TPM
Normalization
DESeq2
updated 23 hours ago by
b.contreras.moreira
▴ 180 • written 1 day ago by
JH
• 0
0
votes
0
replies
75
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
20 hours ago by
rustykb
▴ 20
0
votes
0
replies
83
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
17 hours ago by
NorbertK
• 0
0
votes
0
replies
60
views
Modify plot R mtDNA indel
plot
mtDNA
R
17 hours ago by
marco.barr
▴ 90
0
votes
6
replies
267
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
updated 16 hours ago by
dsull
★ 6.0k • written 1 day ago by
Chen
• 0
0
votes
0
replies
62
views
IGV interpretation for ATM gene for chromosome 11 for a deceased partient suspected of having melanoma
genetic
Variant
predisposition
16 hours ago by
mikemakaveli1
• 0
0
votes
0
replies
65
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
updated 15 hours ago by
Ram
43k • written 16 hours ago by
M.
▴ 30
0
votes
2
replies
123
views
Raw counts using stringtie
stringtie
RNA-seq
updated 15 hours ago by
GenoMax
142k • written 17 hours ago by
ahmad.sajad4541
• 0
0
votes
0
replies
64
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
15 hours ago by
Javier
• 0
0
votes
0
replies
67
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
14 hours ago by
Emilie
• 0
0
votes
1
reply
87
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
updated 13 hours ago by
GenoMax
142k • written 13 hours ago by
Lada
▴ 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 11 hours ago by
swbarnes2
14k • written 12 hours ago by
kalavattam
▴ 190
0
votes
6
replies
281
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 10 hours ago by
swbarnes2
14k • written 18 hours ago by
Erina
• 0
0
votes
0
replies
87
views
Empty table plot using plotGseaTable()
FGSEA
10 hours ago by
Chris
▴ 260
0
votes
1
reply
95
views
visualize GSEA
enrichment
barplot
RNA-seq
GSEA
positive
updated 9 hours ago by
bk11
★ 2.4k • written 11 hours ago by
Rob
▴ 170
0
votes
5
replies
219
views
Easy way to find out which allele is minor allele from bed file?
plink
updated 7 hours ago by
chrchang523
10k • written 16 hours ago by
curious
▴ 750
0
votes
1
reply
172
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
updated 6 hours ago by
chrchang523
10k • written 3 days ago by
8armed
• 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
54
views
HCL database download
database
HCL
human
updated 4 hours ago by
GenoMax
142k • written 4 hours ago by
sooni
▴ 20
46 results • Page
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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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• 0
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▴ 40
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▴ 170
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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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