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84 results • Page
2 of 2
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Rank
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Votes
Replies
0
votes
0
replies
107
views
lncRNA
tcga
lncrna
3 days ago by
jain72744
▴ 10
1
vote
2
replies
355
views
How to remove multiple batch effects from RNA-seq data before limma differential gene expression analysis?
ComBat-seq
limma
RNA-seq
removeBatchEffect
batch-effect
updated 3 days ago by
Ram
43k • written 4 days ago by
t.fortunato.asquini
• 0
0
votes
2
replies
205
views
Output file of samtools flagstat empty
samtools-flagstat
updated 3 days ago by
colindaven
6.4k • written 4 days ago by
ramendra.sarma
• 0
0
votes
4
replies
392
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
3 days ago by
beginner123
• 0
0
votes
2
replies
228
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
3 days ago by
analyst
▴ 50
0
votes
1
reply
202
views
extract viral protein of interest from 10k whole viral genomes
nBLAST
viral-genome
updated 6 days ago by
Ram
43k • written 6 days ago by
Shwetha
• 0
0
votes
0
replies
163
views
Marker Features variance by cluster, sample, and treatment group
Seurat
scATAC-seq
ArchR
updated 6 days ago by
Ram
43k • written 6 days ago by
naomiboldon
• 0
1
vote
3
replies
280
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk
vcf
liftover
updated 6 days ago by
Ram
43k • written 6 days ago by
Omics data mining
▴ 260
0
votes
5
replies
316
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
3 days ago by
SilhouetteQ
• 0
0
votes
1
reply
187
views
Alignment of samples with spike-in
alignment
multimapping
RNA-seq
ChIP-seq
spike-in
updated 6 days ago by
GenoMax
142k • written 6 days ago by
maria.soler
• 0
0
votes
2
replies
291
views
How are score_weights calculated in this code?
single-cell
5 days ago by
carolofharvest
▴ 40
0
votes
1
reply
222
views
How to convert Haps file to vcf file?
pre-phasing
GWAS
imputation
updated 6 days ago by
curious
▴ 750 • written 6 days ago by
SeoGyun
• 0
0
votes
0
replies
156
views
Trouble converting tfam and tped to map and ped files
plink
ped
tfam
tped
map
6 days ago by
Samantha
• 0
0
votes
1
reply
191
views
Microbial Signal Transduction Database
MiST
updated 6 days ago by
zx8754
11k • written 6 days ago by
Shravani
• 0
0
votes
0
replies
144
views
Allele specific expression of imprinted gens from 10x scRNA-seq data
scrna-seq
imprinted
10x
genes
6 days ago by
singcell
• 0
0
votes
1
reply
216
views
When should I use R-MarkDown over R-Script ?
r
rscript
rmarkdown
updated 6 days ago by
ATpoint
82k • written 6 days ago by
Amr
▴ 160
0
votes
2
replies
228
views
LncRNA Nomenclature
ENST
nomenclature
lncrna
GBB
ENSG
6 days ago by
jain72744
▴ 10
3
votes
1
reply
206
views
Question about methylation location
Methylation
WGBS
bisulfide
updated 6 days ago by
dthorbur
★ 2.0k • written 7 days ago by
Eren
• 0
0
votes
0
replies
169
views
How do I calculate SE or P value if I only have BETA
prscsx
beta
se
pvalue
updated 6 days ago by
zx8754
11k • written 7 days ago by
curious_butterfly
• 0
0
votes
2
replies
226
views
Presence of unknown sites in ANNOVAR output file
ANNOVAR
updated 6 days ago by
Ram
43k • written 7 days ago by
sainavyav22
• 0
3
votes
4
replies
316
views
Truncated metadata file report from ENA Portal API
ena
python
6 days ago by
Giulia
• 0
5
votes
7
replies
483
views
RNA seq analysis
DESeq
RNA-seq
1 day ago by
Jacek
▴ 20
1
vote
9
replies
391
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 6 days ago by
i.sudbery
19k • written 9 days ago by
Assa Yeroslaviz
★ 1.8k
0
votes
4
replies
299
views
Correlation Analysis
statistics
methylation
NGS
expression
5 days ago by
Researcher
▴ 30
1
vote
1
reply
170
views
Help with VG Toolkit: VCF Output is Empty
vg
updated 5 hours ago by
Jordan M Eizenga
▴ 460 • written 10 days ago by
sarumonsus
▴ 10
0
votes
2
replies
270
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 6 days ago by
GenoMax
142k • written 13 days ago by
Ximena
• 0
0
votes
2
replies
295
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 4 days ago by
Zhenyu Zhang
★ 1.2k • written 13 days ago by
yahn
• 0
3
votes
3
replies
263
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 3 days ago by
Ram
43k • written 16 days ago by
Adyasha
• 0
0
votes
0
replies
117
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass-spectrometry
Proteins
updated 3 days ago by
Ram
43k • written 17 days ago by
atharvakarkare14
▴ 30
0
votes
0
replies
181
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
deeptools
correlation
2 days ago by
Emily
▴ 20
1
vote
4
replies
411
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 6 days ago by
GenoMax
142k • written 29 days ago by
aniigodwinn
• 0
1
vote
4
replies
499
views
cellranger error message
multiplexing
cellranger
updated 6 days ago by
Max
• 0 • written 3 months ago by
Alivia
▴ 10
0
votes
9
replies
594
views
Using VEP annotation output as the input for a second VEP annotation
Annotation
VEP
VCF
1 day ago by
Arton
▴ 10
0
votes
4
replies
3.6k
views
SNPEff database building error
SNP
updated 3 days ago by
Fungal genetics
• 0 • written 7.1 years ago by
ntyagi654
• 0
84 results • Page
2 of 2
Recent Votes
Comment: Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Answer: Details on salmon index
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Answer: Faster Needleman-Wunsch rapid global alignment of two sequences?
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
Comment: Can I perform a correlation test with 3 biological replicates per condition?
Answer: --normalizeUsing RPGC
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Recent Replies
Comment: GRIDSS: the Genomic Rearrangement IDentification Software Suite
by
dario.garvan
▴ 520
It seems that Alexandrov's [structural variant and copy number signatures][1] estimated by the [SigProfiler software ecosystem][2] aren't c…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
GenoMax
142k
Then you may want to see if a program like `lastz` ([**LINK**][1]) may be useful. [1]: https://github.com/lastz/lastz
Comment: Collect dispersed executable files and run them by using bingo.
by
Ram
43k
What is the purpose of this tool? I have `~/bin` in my $PATH and I soft-link all executables I need to that location so why install a new t…
Comment: Merge clusters in Seurat UMAP
by
bk11
★ 2.4k
Can you try this? library(dplyr) seuratobj@meta.data <- seuratobj@meta.data %>% mutate(seurat_clusters = recode(seurat_clu…
Comment: Merge clusters in Seurat UMAP
by
kilcdincer
▴ 10
Thank you for the response but it does not change anything.
Comment: Merge clusters in Seurat UMAP
by
bk11
★ 2.4k
I have not tested but you could try something like below- seuratobj$seurat_clusters[seuratobj$seurat_clusters==5]=0 seuratobj$seur…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
Gabriel R.
★ 2.9k
I know about it, isn't there a simple C++ static binary?
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
Gabriel R.
★ 2.9k
needle is great! but it does not handle sequences of 100k or so.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
Ram
43k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Comment: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
by
txema.heredia
▴ 130
The point is that you need to feed the ambient algorithm a clustering list as input. This way, it checks for genes present in the soup vs g…
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
swbarnes2
14k
Wait, so the magnitudes of the PCs are in the thousands? That's not normal for RNASeq.
Comment: Help with VG Toolkit: VCF Output is Empty
by
Jordan M Eizenga
▴ 460
What do you get if you use `vg stats -a` on the GAM file?
Comment: About runing Pilon on individual chromosomes when polish draft genome assembly
by
sansan_96
▴ 90
Hello, What approach could you recommend for a large genome (3Gb) with about 10k scaffolds? I'm having problems with RAM when processing t…
Comment: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
by
e.r.zakiev
▴ 210
Very good question and analysis. I personally only tried SoupX so can't weigh in on the comparison. This might be not really the issue here…
Comment: Is there any way to modify this pie chart ?
by
marco.barr
▴ 120
Try following the same logic as the guide which adds the labels about halfway through each pie slice value. Check column's name in script b…
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