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22 results • Page
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1
vote
15
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Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
6 hours ago by
hophuquy0944
• 0
38
votes
12
replies
31k
views
9 follow
How to systematically check if a bam file is truncated
Exomeseq
updated 19 hours ago by
alanh
▴ 170 • written 7.1 years ago by
jonessara770
▴ 240
4
votes
9
replies
419
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch
alignment
22 hours ago by
Gabriel R.
★ 2.9k
1
vote
8
replies
429
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
updated 7 hours ago by
Alex Reynolds
35k • written 4 days ago by
ntsopoul
▴ 60
4
votes
7
replies
459
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
updated 23 hours ago by
marco.barr
▴ 130 • written 2 days ago by
diqixiaoyaoer
▴ 20
0
votes
7
replies
4.3k
views
B allele frequency (BAF)
snp
updated 7 hours ago by
aidangcruickshank
▴ 10 • written 3.7 years ago by
rthapa
▴ 90
0
votes
6
replies
262
views
ComplexHeatmap - How to change fontsize of rowAnnotation
ComplexHeatmap
14 hours ago by
hannes.bongartz
• 0
1
vote
5
replies
296
views
Reconstruction of locus, order contigs
contigs
cluster
alignment
locus
updated 18 hours ago by
dthorbur
★ 2.0k • written 1 day ago by
BATMAN
• 0
1
vote
4
replies
270
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated just now by
Joe
21k • written 9 days ago by
cput
• 0
6
votes
4
replies
292
views
Details on salmon index
Salmon
updated 22 hours ago by
Rob
6.6k • written 2 days ago by
Lorenzo
• 0
3
votes
4
replies
285
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq
patch
freeze
genome
updated 20 hours ago by
Jeremy Leipzig
22k • written 2 days ago by
Ali
• 0
0
votes
4
replies
251
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
3 hours ago by
mavy
▴ 10
0
votes
4
replies
242
views
How to handle duplicated genes in TCGA data?
TCGA
GDC
mRNA
updated 2 hours ago by
txema.heredia
▴ 130 • written 1 day ago by
Ngrin
• 0
0
votes
2
replies
158
views
Trimming tool
Trimmer
tool
updated 15 hours ago by
ntsopoul
▴ 60 • written 17 hours ago by
GeneC
• 0
0
votes
2
replies
148
views
GG Sankey plot
GO
sankey_plot
gglpot
updated 13 hours ago by
LauferVA
4.2k • written 18 hours ago by
ijarne
• 0
1
vote
1
reply
89
views
RNAseq coverage vs depth for transcript isoform expression?
RNAseq
updated 2 hours ago by
Gordon Smyth
★ 7.2k • written 13 hours ago by
marineandriot
• 0
0
votes
1
reply
122
views
Design for complex RNA-Seq experiment using Deseq2
Model.Matrix
RNA-Seq
Limma
DESeq2
edgeR
updated 13 hours ago by
swbarnes2
14k • written 17 hours ago by
Ezequiel
• 0
0
votes
0
replies
75
views
Understanding behaviour of SCTransform in Seurat
Seurat
scRNASeq
normalization
updated 22 hours ago by
GenoMax
142k • written 23 hours ago by
yura.grabovska
▴ 90
0
votes
0
replies
62
views
Cell type annotation mixed with other type cells
cell
annotation.
updated 13 hours ago by
GenoMax
142k • written 14 hours ago by
Long
• 0
0
votes
0
replies
47
views
How can i use ESM-1v ?
VEP
ESM-1v
9 hours ago by
Meto
• 0
0
votes
0
replies
65
views
sci-RNA-seq
cell
single
seurat
sci-rna-seq
counts
16 hours ago by
kilcdincer
▴ 10
0
votes
0
replies
88
views
genomic region of transcription factor
search
HOMER
motif
18 hours ago by
qudrat.nii
▴ 10
22 results • Page
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Recent Votes
Answer: RNAseq coverage vs depth for transcript isoform expression?
Answer: ChatGPT optimized for bioinformatics questions
Comment: ChatGPT optimized for bioinformatics questions
C: How can I perform Differential expression analysis with just one control and one
C: How can I perform Differential expression analysis with just one control and one
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★ 6.0k
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Recent Replies
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 precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167. Our resul…
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…
Comment: How to handle duplicated genes in TCGA data?
by
Ngrin
• 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2
by
swbarnes2
14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
Comment: GG Sankey plot
by
LauferVA
4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
Answer: GG Sankey plot
by
bk11
★ 2.5k
You need to change your data table into a 'long' format. You can do something like this- GOs_childs_recursive <- GOs_childs_recursive …
Answer: Trimming tool
by
ntsopoul
▴ 60
I use Trim Galore which automatically recognizes adaptors. https://github.com/FelixKrueger/TrimGalore Here is the script I am using for…
Answer: Trimming tool
by
GenoMax
142k
There are plenty. `bbduk.sh` from BBMap suite (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/ )…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
bk11
★ 2.5k
Please check out [in this link.][1] [1]: https://github.com/jokergoo/ComplexHeatmap/issues/349
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