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94 results • Page
2 of 2
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Votes
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0
votes
2
replies
138
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
1 day ago by
dtnondorf
• 0
0
votes
1
reply
124
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
165
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 22 hours ago by
Chris Dean
▴ 390 • written 1 day ago by
sovrappensiero
▴ 90
0
votes
1
reply
542
views
HOMER on AWS
HOMER
updated 22 hours ago by
clairechung112
• 0 • written 2.2 years ago by
Bogdan
★ 1.4k
0
votes
0
replies
82
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
20 hours ago by
Jeyong
• 0
0
votes
0
replies
65
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
14 hours ago by
rustykb
▴ 20
0
votes
1
reply
95
views
Downloading older version of a tool
Alignment
tools
updated 13 hours ago by
GenoMax
142k • written 14 hours ago by
Ruqaiya
• 0
0
votes
0
replies
55
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
12 hours ago by
NorbertK
• 0
0
votes
0
replies
50
views
Modify plot R mtDNA indel
plot
mtDNA
R
11 hours ago by
marco.barr
▴ 90
0
votes
0
replies
53
views
IGV interpretation for ATM gene for chromosome 11 for a deceased partient suspected of having melanoma
genetic
Variant
predisposition
10 hours ago by
mikemakaveli1
• 0
0
votes
0
replies
45
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
10 hours ago by
yahn
• 0
0
votes
0
replies
53
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
updated 10 hours ago by
Ram
43k • written 10 hours ago by
M.
▴ 30
0
votes
2
replies
108
views
Raw counts using stringtie
stringtie
RNA-seq
updated 9 hours ago by
GenoMax
142k • written 11 hours ago by
ahmad.sajad4541
• 0
0
votes
0
replies
52
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
9 hours ago by
Javier
• 0
0
votes
0
replies
57
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
9 hours ago by
Emilie
• 0
0
votes
1
reply
71
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
updated 7 hours ago by
GenoMax
142k • written 7 hours ago by
Lada
▴ 30
0
votes
0
replies
39
views
filtering before dada2
metagenomic
bbduk
qiime2
dada2
bioinformatics
5 hours ago by
Valentina
• 0
0
votes
0
replies
42
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
5 hours ago by
Ximena
• 0
0
votes
6
replies
256
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 5 hours ago by
swbarnes2
14k • written 12 hours ago by
Erina
• 0
0
votes
0
replies
79
views
Empty table plot using plotGseaTable()
FGSEA
4 hours ago by
Chris
▴ 260
0
votes
0
replies
33
views
Design matrix Differential expression analysis
expression
designmatrix
analysis
Differential
RNA-sequence
4 hours ago by
SHN
▴ 40
0
votes
5
replies
366
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 6 days ago by
Istvan Albert
100k • written 9 days ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
32
views
Quetion regarding WGCNA
WGCNA
Network
construction
3 hours ago by
deepak180001
• 0
0
votes
0
replies
143
views
Filter low express genes in microarray data
microarray
6 days ago by
Chris
▴ 260
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
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
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
0
votes
0
replies
238
views
Differential accessibility using DiffBinf
diffbind
4 days ago by
Shloka
• 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
0
votes
1
reply
209
views
Finding batch and outlayers
Pca
updated 4 days ago by
christopher medway
▴ 460 • written 5 days ago by
Tigran
• 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
0
replies
106
views
LEfSe
LEfSe
4 days ago by
benkosta
• 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
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
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
214
views
How to update R on ubuntu
installation
update
R
apt-get
4 days ago by
Bosberg
▴ 50
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
331
views
CWl and toil singularity image e.g busybox? Thank you
toil
singularity
updated 4 days ago by
Ram
43k • written 4 months ago by
Fadi
• 0
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
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
0
votes
0
replies
123
views
Using limma in methylation EM-seq?
EM-seq
methylation
4 days ago by
Lluís R.
★ 1.2k
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
2
replies
199
views
What should I consider as FASTA for dataset?
PDB
FASTA
4 days ago by
Nafi
• 0
94 results • Page
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Recent Votes
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
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
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SHN
▴ 40
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Rob
▴ 170
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GenoMax
142k
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curious
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M.
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e.r.zakiev
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Recent Replies
Answer: 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
I need assistance don't know what to do next after signing up
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…
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