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1,000 results • Page
7 of 20
Sort: Rank
Rank
Views
Votes
Replies
3
votes
5
replies
377
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
13 days ago by
Maverick
▴ 10
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 13 days ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
0
votes
2
replies
228
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
13 days ago by
dtnondorf
• 0
3
votes
8
replies
677
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core
16S
amplicon
dada2
ampliseq
updated 9 days ago by
Chris Dean
▴ 410 • written 14 days ago by
sovrappensiero
▴ 100
1
vote
2
replies
269
views
RNA-seq data for deep learning classification
rna-seq
13 days ago by
yahn
• 0
3
votes
8
replies
572
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
9 days ago by
Qroid
▴ 40
0
votes
1
reply
537
views
Loss of 'var' using concatenation of AnnData objects
Scanpy
AnnData
updated 14 days ago by
Hugo
• 0 • written 5 months ago by
Rachel
• 0
0
votes
1
reply
173
views
Provean help
variant
Provean
updated 13 days ago by
Mensur Dlakic
★ 27k • written 14 days ago by
Arun Sai Kumar
• 0
1
vote
1
reply
182
views
Download eQTL data of one specific gene for all tissues from GTEx
eQTL
GTEx
updated 14 days ago by
bk11
★ 2.4k • written 14 days ago by
Jeol
▴ 20
1
vote
1
reply
188
views
Super ehancers
enhancers
updated 14 days ago by
jared.andrews07
★ 16k • written 14 days ago by
Oburah
• 0
4
votes
7
replies
393
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
2 days ago by
Chen
• 0
5
votes
5
replies
314
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA
DADA2
metabarcoding
updated 14 days ago by
atharvakarkare14
▴ 30 • written 14 days ago by
Begonia_pavonina
▴ 150
1
vote
7
replies
485
views
Downsampling long-read BAM files
nanopore
BAM
QC
ONT
downsampling
13 days ago by
eebloom
▴ 80
3
votes
3
replies
361
views
What analysis suitable to identify similarly expressed genes between two samples (treated vs untreated). Contrary to DGE analysis,
Gene-Expression
RNA
NOISeq
DGE
updated 13 days ago by
ATpoint
82k • written 14 days ago by
alifafiq1
• 0
0
votes
0
replies
106
views
Use of annotation of integrated Seurat object in single sample
Seurat
14 days ago by
Bine
▴ 60
0
votes
0
replies
116
views
News:
Beyond beginner R: Advancing your coding skills - September 16-19
Advanced-Coding
Programming
R
updated 14 days ago by
Ram
43k • written 14 days ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
250
views
Subsetting and merging back Seurat Object brings different results
Seurat
14 days ago by
Bine
▴ 60
0
votes
0
replies
175
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
NGS
Genomics
Post-doc
R-loops
updated 14 days ago by
Ram
43k • written 14 days ago by
4r-rtg
• 0
1
vote
1
reply
156
views
Discrepancy in read counts from fastq
downsampling
fastq
updated 14 days ago by
Ram
43k • written 14 days ago by
marco.barr
▴ 120
0
votes
0
replies
105
views
Successfully identified and Masked rpeats using RM. What Next?
sequence
annotation
repeatmasker
illumina
assembly
14 days ago by
Vijith
▴ 30
10
votes
14
replies
744
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 9 days ago by
GenoMax
142k • written 15 days ago by
nicole.kavanagh
• 0
0
votes
1
reply
293
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
updated 14 days ago by
Scooter
▴ 280 • written 21 days ago by
avocado123
• 0
0
votes
0
replies
110
views
Combining Methylation Microarray data from different platforms
Microarray
DNA
EPIC
450K
Methylation
14 days ago by
James
▴ 10
0
votes
1
reply
601
views
Basic stats in hierfstat
Fst
stats
hierfstat
updated 14 days ago by
mdav
• 0 • written 19 months ago by
Zoe
• 0
1
vote
3
replies
280
views
Odd alignment question/finding
Alignment
updated 13 days ago by
barslmn
★ 2.1k • written 14 days ago by
poordumbsillyidiot
• 0
0
votes
1
reply
230
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK
recalibration
updated 14 days ago by
GenoMax
142k • written 14 days ago by
mgranada3
▴ 30
0
votes
0
replies
134
views
Looking for the best way to interpret these data
RNA-seq
ontology
GO
updated 14 days ago by
Ram
43k • written 14 days ago by
Oscar
▴ 10
0
votes
7
replies
630
views
Post-imputation plot
michigan-imputation-server
quality-control
updated 13 days ago by
LChart
3.9k • written 17 days ago by
kl
▴ 10
0
votes
1
reply
241
views
How to find overlap of clusters in two seurat porject
clustering
seurat
updated 15 days ago by
Adam
▴ 30 • written 16 days ago by
J
• 0
1
vote
3
replies
353
views
DESeq2 processing problems
deseq2
R
updated 15 days ago by
ATpoint
82k • written 15 days ago by
jagdish7921
• 0
0
votes
1
reply
798
views
cnetplot category names are too long
clusterprofiler
RNA-Seq
enrichplot
cnetplot
updated 14 days ago by
Ram
43k • written 2.7 years ago by
carov
• 0
0
votes
1
reply
175
views
Mutect2 for mitochondria variant discovery
mutect2
mitochondria
updated 15 days ago by
Ram
43k • written 15 days ago by
ernestine.kubi
• 0
0
votes
0
replies
118
views
Tools to circularise the ion torrent bacterial genome assembly
iontorrent
bacteria
circularise
15 days ago by
VITALA
• 0
1
vote
2
replies
283
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
14 days ago by
rianna.collins
• 0
0
votes
1
reply
202
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated 15 days ago by
i.sudbery
19k • written 15 days ago by
Edmond
• 0
0
votes
0
replies
159
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics
metacyc
enzyme
pathway
genomics
15 days ago by
O.rka
▴ 720
0
votes
1
reply
700
views
after selecting specific GO terms to plot, cneplot is not showing any color for genes, GO terms and only showing lines without nodes.
cneplot
updated 15 days ago by
Ram
43k • written 15 days ago by
Dr Huma Naz
• 0
2
votes
2
replies
307
views
p-value in CIBERSORT
CIBERSORT
p-value
15 days ago by
michelafrancesconi9
▴ 20
0
votes
5
replies
423
views
Telescope issue
Telescope
RNA-seq
updated 15 days ago by
GenoMax
142k • written 15 days ago by
eleven11
• 0
5
votes
6
replies
591
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 16 days ago by
me
▴ 760 • written 17 days ago by
Mariana
▴ 40
1
vote
1
reply
253
views
Adjust pvalue in R with different approach give me all different outcome
statistics
R
p-value
updated 15 days ago by
Ram
43k • written 16 days ago by
Jonathan Yoou
▴ 60
1
vote
2
replies
321
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
15 days ago by
Nafi
• 0
1
vote
3
replies
322
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 15 days ago by
GenoMax
142k • written 16 days ago by
jeffrey.maurer.informatics
• 0
1
vote
3
replies
311
views
ERROR When Using Ensembl Plants Biomart Wget API
biomart
plant
ensembl
10 days ago by
Dora
▴ 10
0
votes
0
replies
180
views
News:
Goodbye, Slow Code? How BioNumpy can Redefine Python’s Role in Bioinformatics!
BioNumPy
Python
NumPy
updated 16 days ago by
Ram
43k • written 16 days ago by
Chakri
• 0
0
votes
2
replies
253
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
9 days ago by
Ahiad Chen Zion
• 0
1
vote
5
replies
369
views
Introduce SNPs on FASTA
simulation
snps
haplotypes
pharmacogenetics
13 days ago by
Riccardo
▴ 10
0
votes
0
replies
143
views
News:
Online course: Meta-analysis in R - last 2 seats left
Meta-Analysis
Statistics
R
updated 16 days ago by
Ram
43k • written 16 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
136
views
Somatic variant calling with Mutect2 using 2 matched-normals for one sample
cancer
mutect
variant-calling
GATK
somatic-variants
updated 16 days ago by
Ram
43k • written 16 days ago by
Alexandros
• 0
0
votes
1
reply
185
views
unable to get feature count results
featureCounts
updated 16 days ago by
Ram
43k • written 16 days ago by
Ravita
• 0
1,000 results • Page
7 of 20
Recent Votes
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
A: How count reads
Answer: Probe annotation file for microarray platform MoGene-1_0-st-v1
Comment: Can 5' and 3' scRNAseq be processed with the same pipeline?
C: Splitting .vcf file
Answer: Grouping datasets in Seurat
Answer: How should I make kallisto indexes?
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Recent Awards •
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Popular Question
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carlopecoraro2
★ 2.5k
Scholar
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GenoMax
142k
Popular Question
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ben@f
▴ 20
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Recent Replies
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 : library(ggplot2) libr…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
sorry for that, this is first time i use it.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
thank sir, i will check it again
Comment: In one PCA plot, can I calculate the percentage of different factors that contri
by
diqixiaoyaoer
▴ 10
Ok, I will response to you here as soon as possible.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
How much memory do you have available? For `nt` database you are going to need 30-40G minimum. You may simply be running out of memory.
Comment: Can 5' and 3' scRNAseq be processed with the same pipeline?
by
ev97
▴ 20
Noted! Thanks very much for your help!
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
i'm using linux. I was use 3 file.fasta to debug and it is nucleotide file, and my blast -h still work > (/data/quyho/tools/mgs2amr_tool…
Answer: Details on salmon index
by
Rob
6.5k
Hi Lorenzo, Thanks for your question. First, I'd like to clarify that several substantial updates have been made to salmon since its …
Comment: Can 5' and 3' scRNAseq be processed with the same pipeline?
by
yura.grabovska
▴ 90
sc/snRNASeq tends to have differences in things like mitochondrial genes etc, which you can account for using tools like SCTransform but in…
Comment: Why does assigning genes with biomart give me different values than using a tran
by
bioinfo
▴ 150
Thank you! I ended up using the transcripts_to_genes instead of biomart.
Comment: How can I calculate the OS of each patient?
by
ATpoint
82k
Please be specific. Which TCGA subset, what did you try? Show code.
Answer: mitochondrial genome assembly pipeline
by
shelkmike
★ 1.2k
A good tool for mitochondrial genome assembly is GetOrganelle (https://github.com/Kinggerm/GetOrganelle)
Comment: getting exon coordinates
by
Ram
43k
Please do not use `bioinformatics` as a tag unless your post in about the field of bioinformatics itself.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
Ram
43k
I've removed unneccessary tags - `meta` and `how-to` don't apply to this post at all, and the `forum` tag is not in use anymore.
Comment: Difference in number of reads when using duplex and simplex base calling with Do
by
GenoMax
142k
I assume you have posted this in nanopore community and/or on the dorado issues page on GitHub. Please come back and post an update once yo…
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