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34 results • Page
1 of 1
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Votes
Replies
3
votes
6
replies
194
views
Which file and data structure is used to create volcano plot from scRNA-Seq experiment?
plot
Volcano
6 hours ago by
Chris
▴ 60
3
votes
2
replies
1.5k
views
parsing the samtools view out put
RNA-Seq
updated 6 hours ago by
Ram
37k • written 7.7 years ago by
fi1d18
★ 4.1k
2
votes
12
replies
4.1k
views
Adding barcodes to forward and reverse reads after sequencing
obitools
barcoding
next-gen-sequencing
updated 11 hours ago by
Ram
37k • written 7.7 years ago by
cmogren
▴ 20
2
votes
7
replies
6.6k
views
Bowtie2 run out of memory
software-error
alignment
bowtie2
updated 12 hours ago by
Ram
37k • written 7.7 years ago by
anon
▴ 50
1
vote
0
replies
2.0k
views
Definition of splicing eQTLs in RNA-Seq and arrays
genome
RNA-Seq
snp
updated 12 hours ago by
Ram
37k • written 7.7 years ago by
User 7754
▴ 250
1
vote
1
reply
73
views
bwa mem duration?
performance
mapping
bwa
updated 14 hours ago by
ATpoint
68k • written 14 hours ago by
lacb
▴ 30
0
votes
0
replies
35
views
SpliceAi same variant , different score
SpliceAi
updated 5 hours ago by
Pierre Lindenbaum
152k • written 5 hours ago by
vvasta
• 0
0
votes
1
reply
140
views
Remove duplicates in multifasta, where entries are paired
bash
python
updated 13 hours ago by
dthorbur
▴ 260 • written 1 day ago by
SaltedPork
▴ 170
0
votes
0
replies
121
views
How to use gseapy after scanpy?
gsea
single
cell
enrichR
gseapy
13 hours ago by
bioinfo
▴ 20
0
votes
0
replies
1.7k
views
Question regarding sample size in SNPRelate Package in R
snprelate
snptree
SNP
snpgdsDrawTree
updated 8 hours ago by
Ram
37k • written 7.7 years ago by
ayang
• 0
0
votes
3
replies
2.2k
views
Limma, lmFit, array weight
R
updated 9 hours ago by
Ram
37k • written 7.7 years ago by
jl.juluan
• 0
0
votes
1
reply
69
views
Diffbind losing peaks when going from small to larger consensus peak set
DiffBind
3 hours ago by
tara.mcintyre
• 0
0
votes
2
replies
99
views
cellranger-arc mkfastq Error: bcl2fastq was killed with signal -11
bcl2fastq
cellranger-arc
mkfastq
cellranger
9 hours ago by
Yingying
• 0
0
votes
1
reply
103
views
Gene ontology with locus tags
ontology
locus
gene
tags
updated 14 hours ago by
dthorbur
▴ 260 • written 16 hours ago by
sea.joson
▴ 10
0
votes
4
replies
245
views
HTSeq error processing GFF file
HTSeq
GFF
GTF
11 hours ago by
ibq.enriquepola
• 0
0
votes
0
replies
1
view
To batch correct or analyse separately?
scRNA-seq
batch
correction
just now by
bompipi95
▴ 50
0
votes
5
replies
2.4k
views
Question: How to compare the gene expression signature of Primary tumor cell and normal cancer cell
genome
gene expression
Page
updated 12 hours ago by
Ram
37k • written 7.8 years ago by
Naresh
▴ 60
0
votes
7
replies
327
views
CoveragePlot in Signac from MACS2 Object
Signac
scATAC-seq
updated 13 hours ago by
seidel
10k • written 1 day ago by
bioinformatics.girl
• 0
0
votes
0
replies
53
views
What is the difference between gseapy.prerank and gseapy.gsea?
gseapy
gsea
13 hours ago by
bioinfo
▴ 20
0
votes
6
replies
213
views
STAR is running but .sam file size does not increase after hours mapping
STAR
RNA-seq
mapping
SAM
updated 15 hours ago by
GenoMax
125k • written 17 hours ago by
luzglongoria
▴ 40
0
votes
1
reply
67
views
Converting large GSM from GEOquery into a minfi or limma workable set
minfi
methylation
limma
GEOquery
R
updated 13 hours ago by
Basti
★ 1.3k • written 14 hours ago by
Edward E-B
• 0
0
votes
0
replies
61
views
PLINK2 selecting variants based on INFO score
plink2
12 hours ago by
m.c.roozen
• 0
0
votes
0
replies
2.9k
views
bowtie2 output all aligned reads from paired alignment (even unconcordant pairs or single reads)
Assembly
bowtie2
SAM
alignment
BAM
updated 12 hours ago by
Ram
37k • written 7.7 years ago by
JV
▴ 450
0
votes
1
reply
4.3k
views
Convert exonerate output to EVM gff3 format error
evidencemodeler
evm
gff3
exonerate
updated 13 hours ago by
Ram
37k • written 7.7 years ago by
sun.nation
▴ 130
0
votes
0
replies
74
views
Unrooted consensus tree [Bio.Phylo]
consensus
phylo
biopython
11 hours ago by
Jimpix
▴ 10
0
votes
1
reply
107
views
Clustering and dynamic tree cutting
dynamicTreeCut
Clustering
data
RNAseq
cutreeDynamic
updated 15 hours ago by
andres.firrincieli
3.1k • written 17 hours ago by
harish
• 0
0
votes
2
replies
2.8k
views
Bismark out put in IGV
IGV
bisulfite-seq
updated 7 hours ago by
Ram
37k • written 7.7 years ago by
kanwarjag
★ 1.2k
0
votes
1
reply
90
views
RNA Editing data from RNA-seq
Editing
RNA
updated 8 hours ago by
Juke34
7.5k • written 9 hours ago by
Genetics
• 0
0
votes
5
replies
4.3k
views
Error during Trinity running with the recent version?
Assembly
next-gen
RNA-Seq
updated 10 hours ago by
Ram
37k • written 7.7 years ago by
seta
★ 1.7k
0
votes
0
replies
57
views
want the codes for cuffdiff , NIOSeq , bayseq to perform DEGs.
DEGs
updated 8 hours ago by
ATpoint
68k • written 8 hours ago by
rupali
• 0
0
votes
0
replies
46
views
GSEA multiple group analysis
gsea
single-cell
7 hours ago by
piotto
▴ 10
0
votes
0
replies
1.7k
views
Get a CSI-BLAST PSSM
PSI-BLAST
CS-BLAST
PSSM
Protein
updated 6 hours ago by
Ram
37k • written 7.7 years ago by
ddofer
▴ 30
0
votes
1
reply
2.4k
views
OpenSNP and SNP position information
OpenSNP
updated 6 hours ago by
Ram
37k • written 7.7 years ago by
bfeeny
▴ 50
0
votes
0
replies
35
views
Protocol to detect chromosomal ploidy from WGS VCF?
wgs
ploidy
5 hours ago by
optimistsso4co3
▴ 100
34 results • Page
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Recent Votes
Answer: Using Seurat function `FindMarkers` to find differentially expressed genes betwe
C: Which genome files to use for STAR?
Answer: Remove mitochondrial reads from BAM files
Comment: translate CDS to prot formatted with nt nubers
Comment: Analyzing bulk RNA-seq
Comment: Analyzing bulk RNA-seq
Answer: How can I convert this pairwise format to fasta?
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Recent Replies
Comment: Diffbind losing peaks when going from small to larger consensus peak set
by
tara.mcintyre
• 0
I'm now realizing it might be due to the filter parameter being set =1 when I run dba.count because when I set it to 0, all of the peaks ar…
Answer: Obtaining every"Protein ID" from a genome in OMA
by
clement.train
▴ 40
Hello, It seems that the current download is limited to 100 genes on the genomes pages, we will increase this limit to the extent of ea…
Comment: DNA methylation (RRBS/WGBS) prediction from DNA sequence (WGS)
by
Lalaland
▴ 10
Thank you very much, Matthias! I will definitely check those links out myself!
Comment: RNA Editing data from RNA-seq
by
Juke34
7.5k
What tool did you look at ?
Comment: want the codes for Deseq2 to perform DEGs.
by
rupali
• 0
thanks for help
Comment: cellranger-arc mkfastq Error: bcl2fastq was killed with signal -11
by
Yingying
• 0
Hi, Yes I've uploaded the diagnostic file to 10x support already, but haven't got any response yet.
Comment: cellranger-arc mkfastq Error: bcl2fastq was killed with signal -11
by
GenoMax
125k
You may want to contact 10x tech support. When this process failed it must have created a diagnostic archive. You also get a message about …
Answer: How to merge unique/non overlapping genes between 2 gene model GFF3 files?
by
jv
▴ 780
`bedtools intersect -v` is one option for identifying the unique genes from the older gene model. <https://bedtools.readthedocs.io/en/lates…
Comment: Alien-hunter outputs
by
schlogl
▴ 130
@GenoMax Hope this helps...Thank you
Comment: DESeq2 results function runs very slow on Windows 10
by
ATpoint
68k
Does it go away if you remove the `parallel` from `results()`? After all, it is the `DESeq()` function that is the bottleneck when n is lar…
Comment: HTSeq error processing GFF file
by
ibq.enriquepola
• 0
enrique@L:~/bioinformatica/index/prueba$ head -n 997531 GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_genomic.gff|tail -n 1 NC_007982.1 Ref…
Comment: Which file and data structure is used to create volcano plot from scRNA-Seq expe
by
Chris
▴ 60
Thank you for your help! I got an error that I could not find the solution on the Internet: library(EnhancedVolcano) Loading required…
Comment: HTSeq error processing GFF file
by
barslmn
★ 1.2k
I guess you can try to replace the "?" to a "." Also, you can copy and paste text instead of the screenshots?
Answer: DESeq2 results function runs very slow on Windows 10
by
Istvan Albert
96k
Note the following: https://support.bioconductor.org/p/115415/ it looks like it has to do with the Parallel=TRUE flag
Comment: DESeq2 results function runs very slow on Windows 10
by
GenoMax
125k
> there is a massive difference in performance between them. It still is taking only one minute.
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