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15 results • Page
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6
views
Tool:
Sequence alignment on split read event such as inversion, duplication and complex nested events.
minimap
alignment
NGMLR
11 minutes ago by
micah
• 0
0
votes
0
replies
31
views
problems in installing rDock
rDock
make
Installation
Error
3 hours ago by
Rodolfo Adrián
• 0
1
vote
6
replies
1.4k
views
CellRanger output more cells than specified using --force-cells? Why?
scRNA-seq
cellranger
updated 3 hours ago by
scideas
▴ 30 • written 8 months ago by
rohitsatyam102
▴ 870
0
votes
0
replies
26
views
seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from input file
subseq
seqtk
extractionproblem
3 hours ago by
KHURRAM SHAHZAD
• 0
1
vote
2
replies
632
views
Checking chromosome builds for genotyping data
GWAS
Liftover
PLINK
updated 5 hours ago by
Muhammad
• 0 • written 2.6 years ago by
mari.johnson
• 0
1
vote
1
reply
262
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 10 hours ago by
nguyenn6
• 0 • written 12 weeks ago by
star
▴ 10
0
votes
0
replies
71
views
Buzzled by retrieving metadata on bioprojects for an organism using "rentrez" package
R
updated 16 hours ago by
Pierre Lindenbaum
161k • written 16 hours ago by
Mohamed Samir
▴ 20
0
votes
0
replies
79
views
Tera-scale metagenomic coassembly tool
co-assembly
Metagenomics
19 hours ago by
Moinuddin
• 0
0
votes
1
reply
112
views
Broad and Narrow peaks
ATAC
ChIP
seq
updated 21 hours ago by
ATpoint
82k • written 21 hours ago by
Jacek
▴ 20
2
votes
1
reply
181
views
RNAseq coverage vs depth for transcript isoform expression?
RNAseq
updated 10 hours ago by
Gordon Smyth
★ 7.2k • written 1 day ago by
marineandriot
• 0
1
vote
1
reply
153
views
constructing pangenome through psvcp
psvcp
pangenome
18 hours ago by
analyst
▴ 50
1
vote
16
replies
733
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
updated 18 hours ago by
GenoMax
142k • written 3 days ago by
hophuquy0944
• 0
0
votes
5
replies
297
views
calculating genomic coverage/ base overlap in R
genomics
updated 20 hours ago by
1769mkc
★ 1.2k • written 3 days ago by
Xbox_27
• 0
1
vote
4
replies
316
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 21 hours ago by
Joe
21k • written 10 days ago by
cput
• 0
0
votes
2
replies
296
views
Traveler with Infernal mapping failed
r2dt
updated 11 hours ago by
anton.i.petrov
• 0 • written 3 months ago by
Larissa
• 0
15 results • Page
1 of 1
Recent Votes
Interpreting the Jackstraw plot of Seurat
A: How is the design in DESeq2 work?
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
Answer: RNAseq coverage vs depth for transcript isoform expression?
constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
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Recent Awards •
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Popular Question
to
scideas
▴ 30
Popular Question
to
Muhammad
• 0
Popular Question
to
synat.keam
▴ 100
Scholar
to
jv
★ 1.8k
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syedahamdani94
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▴ 260
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★ 6.0k
Recent Replies
Answer: CellRanger output more cells than specified using --force-cells? Why?
by
scideas
▴ 30
I actually had this same issue with CellRanger v7- turns out that since you have 2 species in your mapping reference, CellRanger is forcing…
Answer: Checking chromosome builds for genotyping data
by
Muhammad
• 0
Assume you have genotype data in Plink format. (G.bed, G.bim, G.fam) Download some reference panel data in Plink format (R.bed, R.bim, R.f…
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors)
by
nguyenn6
• 0
did you ever figure it out? i'm having the same issue.
Comment: Traveler with Infernal mapping failed
by
anton.i.petrov
• 0
Hi Larissa! I am the lead developer of R2DT and I've just noticed this question. Could you please email help@r2dt.bio with your input seque…
Comment: constructing pangenome through psvcp
by
analyst
▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
Comment: calculating genomic coverage/ base overlap in R
by
1769mkc
★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks
by
ATpoint
82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner
by
Joe
21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression?
by
Gordon Smyth
★ 7.2k
See the exploration of isoform estimation precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167.…
Comment: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA
by
mavy
▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object
by
Alex Reynolds
35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF)
by
aidangcruickshank
▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
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