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537 results • Page
1 of 11
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Views
Votes
Replies
11
votes
22
replies
4.2k
views
No significant DEG: A request to double check my commands for limma.
limma
differential-gene-expression
updated 15 days ago by
Ram
43k • written 5.0 years ago by
RNAseqer
▴ 260
13
votes
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva
combat
batch-effect
updated 8 days ago by
Ram
43k • written 6.8 years ago by
lessismore
★ 1.3k
2
votes
18
replies
1.6k
views
error when running phg create-maf-vcf to build a built practical haplotype graph (v2)
pangenome
phg_v2
plants
PHG
23 days ago by
b.contreras.moreira
▴ 170
4
votes
13
replies
856
views
RNAseq of primary tumor and metastases in two different organ
metastases
RNA-seq
DEG
R
updated 8 days ago by
BioinfGuru
★ 1.7k • written 13 days ago by
matteo.levorato
• 0
2
votes
12
replies
726
views
Nanopore data filtering using fastp
fastp
nanopore
27 days ago by
emilydolivo97
▴ 10
3
votes
12
replies
488
views
struggle to get fasta files from ucsc goldenPath
ucsc
getfasta
fasta
22 days ago by
Lila M
★ 1.2k
4
votes
12
replies
3.5k
views
How to read VCF (v4.1) file? (student project) (samtools version 0.1.19)
variant-calling
samtools
VCF
BCF
updated 29 days ago by
Ram
43k • written 5.5 years ago by
c.clarido
▴ 110
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 8 days ago by
Ram
43k • written 7.4 years ago by
linda
• 0
8
votes
10
replies
692
views
bash script
whole-genome-sequencing
updated 9 days ago by
Ram
43k • written 17 days ago by
bestone
▴ 30
0
votes
10
replies
369
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
1 day ago by
atowns21
• 0
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma
microarray
DEA
batch-effect
updated 7 days ago by
Ram
43k • written 4.7 years ago by
asalimih
▴ 60
2
votes
10
replies
819
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated 27 days ago by
Ram
43k • written 9 weeks ago by
Sky
▴ 10
0
votes
10
replies
620
views
Nextflow ERROR : Timeout waiting for connection from pool
nextflow
24 days ago by
dzisis1986
▴ 70
2
votes
9
replies
800
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 1 day ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
4
votes
9
replies
568
views
variant calling
variant-calling
updated 21 days ago by
Ram
43k • written 22 days ago by
dalibenam64
• 0
0
votes
9
replies
1.2k
views
Normalization across different single cell RNAseq experimetns
global-scaling
single-cell
scRNA-seq
batch-effect
updated 8 days ago by
Ram
43k • written 3.9 years ago by
jmah
▴ 20
0
votes
9
replies
577
views
99.9999% of Q30 bases is normal?
RNA-seq
fastp
updated 13 days ago by
LauferVA
4.2k • written 14 days ago by
Aki
▴ 10
0
votes
9
replies
477
views
Low number of both surviving reads after trimming
trimmomatic
trimming
27 days ago by
Jay
• 0
0
votes
8
replies
281
views
Error in cnetplot enrichplot package
R
updated 2 days ago by
Ram
43k • written 2 days ago by
Farhad
• 0
5
votes
8
replies
3.7k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression
RNA-seq
gene-ontology
updated 15 days ago by
Ram
43k • written 6.5 years ago by
firestar
★ 1.6k
1
vote
8
replies
3.4k
views
Best way to address different batches of RNA-seq
sequence
RNA-Seq
RPKM
Fold-Change
batch-effect
updated 7 days ago by
Ram
43k • written 7.0 years ago by
tud55122
▴ 20
0
votes
8
replies
5.3k
views
8 follow
cellranger mkref failed
next-gen-sequencing
software-error
RNA-seq
updated 15 days ago by
EricYang
• 0 • written 4.7 years ago by
Dan
▴ 180
0
votes
8
replies
518
views
STAR aligner options
STAR
27 days ago by
theophile
• 0
0
votes
7
replies
411
views
Salmon Quantification in Alignment based-mode
Salmon
RNA-seq
TPM
updated 28 days ago by
GenoMax
141k • written 28 days ago by
Patadu94
• 0
4
votes
7
replies
558
views
Can any JBrowse2 tracks show multiple colors for reads at different nucleotide positions?
JBrowse
JBrowse2
updated 23 days ago by
cmdcolin
★ 3.8k • written 26 days ago by
I0110
▴ 140
5
votes
7
replies
2.7k
views
DESeq2 for differential gene expression on GTEx dataset
differential-gene-expression
RNA-Seq
GTex
DESeq2
updated 15 days ago by
Ram
43k • written 6.4 years ago by
vikram
▴ 10
0
votes
7
replies
6.0k
views
Pre-processing of RNA-Seq data for WGCNA
RNA-Seq
WGCNA
removeBatchEffect
DESeq2
updated 8 days ago by
Ram
43k • written 7.6 years ago by
gokce.ouz
▴ 70
4
votes
7
replies
2.4k
views
Batch effects vs biological variables
Batch-effect
DESeq2
combat_seq
updated 16 days ago by
Ram
43k • written 3.7 years ago by
l.uva
▴ 20
4
votes
7
replies
540
views
DESeq2 Multifactor Design
RNA-seq
DESeq2
updated 11 days ago by
Ram
43k • written 12 days ago by
AHerik
▴ 20
1
vote
7
replies
888
views
GATK Mutect2 Input files reference and features have incompatible contigs: No overlapping contigs found.
hg19
Mutect2
GATK
Variant-Calling
updated 29 days ago by
Ram
43k • written 9 months ago by
Manuel Sokolov Ravasqueira
▴ 100
0
votes
7
replies
398
views
DESeq: too low p-value for RNAseq
R
DESeq
p-value
RNA-seq
FDR
updated 20 days ago by
Papyrus
★ 2.9k • written 20 days ago by
doramora
▴ 10
2
votes
7
replies
805
views
Removing duplicates
duplicates
ONT
minimap2
updated 6 days ago by
joe
▴ 510 • written 7 days ago by
quentinperriere
• 0
3
votes
6
replies
4.1k
views
how do Differential gene expression analysis by Salmon output
differential-gene-expression
Salmon
updated 15 days ago by
Ram
43k • written 5.5 years ago by
lkianmehr
▴ 100
2
votes
6
replies
859
views
Batch effect correction with cell type enrichment analysis
limma
RNA-seq
r
batch-effect
updated 8 days ago by
Ram
43k • written 19 months ago by
JACKY
▴ 140
2
votes
6
replies
397
views
create a gene count matrix csv file from seurat object
Seurat
sparseMatrix
16 days ago by
jkim
▴ 170
0
votes
6
replies
547
views
PacBio adapters in transcriptome assembly from short read data?
adapter
transcriptome
sequencing
pacbio
vecscreen
9 days ago by
Dunois
★ 2.5k
2
votes
6
replies
629
views
Overlapping and merging ChIP-seq peaks
MACS2
HOMER
ChIP-seq
peak-calling
updated 22 days ago by
Ram
43k • written 4 months ago by
zea
• 0
0
votes
6
replies
1.0k
views
Considering that the basal expression level is not 0 for the calculation of the differential expression
DESEQ2
RNA-Seq
Differential-gene-Expression
updated 15 days ago by
Ram
43k • written 5.7 years ago by
Pin.Bioinf
▴ 340
1
vote
6
replies
1.6k
views
How can Differentially Expressed Genes be found by limma package after removing batch effect by ComBat function in sva package?
limma
sva
batch-effect
R
updated 9 days ago by
Ram
43k • written 3.8 years ago by
amirmehrgou
▴ 10
5
votes
6
replies
390
views
7 follow
Seeking Help with Unexpected MA Plot Output
MAplot
RNAseq
Rstudio
updated 22 days ago by
Istvan Albert
100k • written 23 days ago by
Pumla
• 0
0
votes
6
replies
613
views
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data?
differential-expression
RNA-Seq
ONT
Nanopore
updated 15 days ago by
Ram
43k • written 4 months ago by
tw_140
• 0
0
votes
6
replies
423
views
Use of Kraken output for functional analysis
metagenomics
kraken
shotgun
updated 1 day ago by
gv
• 0 • written 23 days ago by
Srinka
▴ 20
0
votes
6
replies
456
views
Error in running Mauve alignner in Ubuntu 20.04
java
linux
aligner
mauve
15 days ago by
marongiu.luigi
▴ 710
4
votes
6
replies
832
views
bwa mem hangs after a few thousand reads
bwa
alignment
variant-calling
bwa-mem
updated 22 days ago by
Ram
43k • written 4 months ago by
cee28
▴ 30
3
votes
6
replies
2.4k
views
How to adjust by multiple variables using ComBat-Seq?
CombatSeq
combat
rna-seq
sva
batch-effect
updated 8 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
0
votes
5
replies
5.9k
views
Calculate Radius of Gyration [python 3]
biopython
PDB
Radius of Gyration
python
protein
updated 4 days ago by
ndm1096
• 0 • written 6.5 years ago by
ac.research
▴ 30
0
votes
5
replies
415
views
Error running local blastn in R using system2
blastn
NCBI
R
26 days ago by
Harrison
• 0
0
votes
5
replies
273
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
22 hours ago by
njornet
▴ 20
2
votes
5
replies
668
views
samtools mpileup taking too long
Bam
samtools
sam
alignment
updated 19 days ago by
Ram
43k • written 6 weeks ago by
K
• 0
2
votes
5
replies
428
views
Marking duplicates using UMIs
Deduplication
UMI
updated 3 days ago by
i.sudbery
19k • written 4 days ago by
Lipika
• 0
537 results • Page
1 of 11
Recent Votes
Answer: Fetch table from clinvar database according to a list of rsid
Comment: Fetch table from clinvar database according to a list of rsid
Comment: Adding CB tag to bam file
Comment: alignment result
Comment: clustalo - align milions of short seq, memory issue
Answer: clustalo - align milions of short seq, memory issue
Comment: downloading genomes in fasta format from accession ids
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Recent Replies
Answer: Finding orthologs between genome error
by
Adrian Altenhoff
★ 1.1k
Hi, thanks for letting us know. In a recent software update, we introduced a problem with the written splice information in the cached …
Comment: Fetch table from clinvar database according to a list of rsid
by
ashaneev07
▴ 20
so which one should i prefer? i don't need the entire results i need the condition-Germline table only. (for eg:-from, https://www.ncbi.nlm…
Comment: To get p-values for the TPM
by
dsull
★ 5.8k
OK, not sure why your intention is to use RSEM p-values for, but at least tell us the commands you ran then otherwise how are we supposed t…
Comment: Fetch table from clinvar database according to a list of rsid
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: different FeatureCounts output for the same data
by
sehriban.buyukkilic
▴ 10
Sure, I'll inquire about the version of Rsubread. I'll keep you posted if it works :) Thanks
Comment: different FeatureCounts output for the same data
by
sehriban.buyukkilic
▴ 10
Yeah, let me show you my featureCounts result, it looks like this. It's too low. [1]: /media/images/eb8293fe-e6ae-4b02-92e2-0ba2075b
Comment: Adding CB tag to bam file
by
Pierre Lindenbaum
161k
samtools addreplacerg is for read groups. This is not what OP asked.
Comment: Adding CB tag to bam file
by
Maria
• 0
When I try ``` samtools addreplacerg -r "@CB\tID:$cell" -o $cell.bam $LINE``` the CB tag gets add to the header, but the tag in every line …
Answer: Figures are disappeared from html report of SnpEff
by
Pierre Lindenbaum
161k
the remote website providing the javascript or/and the images is down or you're now behind a proxy. Check the firefox console: https://fire…
Comment: Fetch table from clinvar database according to a list of rsid
by
Pierre Lindenbaum
161k
ah ! and your code doesn't work because clinvar ID is not a rs-ID.
Answer: Fetch table from clinvar database according to a list of rsid
by
Pierre Lindenbaum
161k
$ cat input.rs rs11203366 rs11203367 rs874881 rs776453694 rs80324279 rs324420 rs112766203 wget -…
Comment: Highest variable features in single cell data
by
ATpoint
82k
> and these cells are not even in a single cluster. What does this mean? If you run clustering on all cells then every cell is assigned t…
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas
by
Bertalan_Takacs
▴ 90
Yes, I can tell that, but as far as I see it doesn't contain any other information about the genomes, such as if they were representative i…
Answer: Hide positions in alignment with 99% "–" characters to ignore single sequence in
by
b.contreras.moreira
▴ 170
You can try <https://github.com/inab/trimal>
Comment: To get p-values for the TPM
by
VITALA
• 0
yes i want what rsem does and i did try with prior-enhanced option/pRSEM, but i think pRSEM is for chipseq data
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