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78 results • Page
1 of 2
Sort: replies
Rank
Views
Votes
Replies
1
vote
14
replies
616
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
15 hours ago by
hophuquy0944
• 0
0
votes
9
replies
599
views
Using VEP annotation output as the input for a second VEP annotation
Annotation
VEP
VCF
1 day ago by
Arton
▴ 10
1
vote
9
replies
257
views
zero TPM for many gene including housekeeping when using kallisto
RNAseq
4 hours ago by
ashkan
▴ 160
5
votes
7
replies
489
views
RNA seq analysis
DESeq
RNA-seq
2 days ago by
Jacek
▴ 20
0
votes
5
replies
318
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
4 days ago by
SilhouetteQ
• 0
0
votes
5
replies
281
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmerge
bbmap
updated 1 day ago by
GenoMax
142k • written 2 days ago by
chrisk
• 0
0
votes
5
replies
161
views
ComplexHeatmap - How to change fontsize of rowAnnotation
ComplexHeatmap
updated 2 hours ago by
bk11
★ 2.5k • written 6 hours ago by
hannes.bongartz
• 0
1
vote
5
replies
248
views
Reconstruction of locus, order contigs
contigs
cluster
alignment
locus
updated 3 hours ago by
dthorbur
★ 2.0k • written 21 hours ago by
BATMAN
• 0
0
votes
4
replies
399
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
4 days ago by
beginner123
• 0
0
votes
4
replies
258
views
Galaxy StringTie error
stringtie
galaxy
3 days ago by
trkfs
• 0
1
vote
4
replies
345
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 2 days ago by
Juke34
8.6k • written 4 days ago by
Vijith
▴ 30
0
votes
4
replies
254
views
Merge clusters in Seurat UMAP
seurat
umap
12 hours ago by
kilcdincer
▴ 10
0
votes
4
replies
303
views
Correlation Analysis
statistics
methylation
NGS
expression
6 days ago by
Researcher
▴ 30
0
votes
4
replies
3.6k
views
SNPEff database building error
SNP
updated 3 days ago by
Fungal genetics
• 0 • written 7.1 years ago by
ntyagi654
• 0
1
vote
3
replies
285
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk
vcf
liftover
updated 6 days ago by
Ram
43k • written 7 days ago by
Omics data mining
▴ 260
3
votes
3
replies
268
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 3 days ago by
Ram
43k • written 17 days ago by
Adyasha
• 0
0
votes
3
replies
343
views
Snakemake wrapper issue
fastqc
snakemake
updated 3 days ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
0
votes
3
replies
161
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
2 days ago by
Esraa
• 0
0
votes
3
replies
196
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
updated 4 hours ago by
andres.firrincieli
3.6k • written 1 day ago by
mavy
▴ 10
0
votes
3
replies
202
views
How to access GWAVA software of data
GWAVA
updated 3 days ago by
GenoMax
142k • written 3 days ago by
nonaddldy
▴ 10
0
votes
3
replies
228
views
Sam file Header problem
Sam
Header
problem
file
updated 13 hours ago by
Pierre Lindenbaum
161k • written 1 day ago by
saifulislam99121
• 0
0
votes
2
replies
153
views
How to generate table_annovar from VCF input?
vcf
annovar
updated 12 hours ago by
Pierre Lindenbaum
161k • written 19 hours ago by
melissachua90
▴ 70
0
votes
2
replies
189
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
2 days ago by
melissa.joubert
• 0
0
votes
2
replies
210
views
Output file of samtools flagstat empty
samtools-flagstat
updated 4 days ago by
colindaven
6.4k • written 5 days ago by
ramendra.sarma
• 0
3
votes
2
replies
189
views
Publish a Letter in higher impact vs Research article in lower impact
Article
Letter
Journal
updated 4 days ago by
ATpoint
82k • written 4 days ago by
jennyp0706
• 0
1
vote
2
replies
359
views
How to remove multiple batch effects from RNA-seq data before limma differential gene expression analysis?
ComBat-seq
limma
RNA-seq
removeBatchEffect
batch-effect
updated 4 days ago by
Ram
43k • written 5 days ago by
t.fortunato.asquini
• 0
1
vote
2
replies
225
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
1 day ago by
bioinfo
▴ 150
0
votes
2
replies
294
views
How are score_weights calculated in this code?
single-cell
6 days ago by
carolofharvest
▴ 40
0
votes
2
replies
296
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 4 days ago by
Zhenyu Zhang
★ 1.2k • written 14 days ago by
yahn
• 0
0
votes
2
replies
176
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
3 days ago by
IdaHao0921
• 0
2
votes
2
replies
195
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 1 day ago by
Ram
43k • written 1 day ago by
txema.heredia
▴ 130
0
votes
2
replies
231
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
4 days ago by
analyst
▴ 50
0
votes
1
reply
152
views
Add line under stat test
stats
R
updated 17 hours ago by
Nyksubuz
▴ 20 • written 2 days ago by
Ghada
• 0
0
votes
1
reply
162
views
consensus sequence calling
consensus
updated 4 days ago by
bk11
★ 2.5k • written 4 days ago by
Ghada
• 0
0
votes
1
reply
149
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences
Demuxlet
updated 3 days ago by
Ram
43k • written 4 days ago by
eking28
• 0
0
votes
1
reply
161
views
How to process Bulk WES data?
WES
WGS
updated 3 days ago by
GenoMax
142k • written 4 days ago by
wyuan37
• 0
0
votes
1
reply
161
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 3 days ago by
GenoMax
142k • written 4 days ago by
cedric.blais
• 0
1
vote
1
reply
147
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 3 days ago by
Ram
43k • written 3 days ago by
kilcdincer
▴ 10
0
votes
1
reply
146
views
Polish a large genome with Pilon
Pilon
Pacbio
Polish
Illumina
2 days ago by
sansan_96
▴ 90
0
votes
1
reply
139
views
Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
annotation
vcf
vep
zygosity
deepvariant
2 days ago by
asalimih
▴ 60
0
votes
1
reply
162
views
What's next after GATK variant calling pipeline?
GATK
pipeline
figures
DNA-seq
updated 1 day ago by
Michael
54k • written 2 days ago by
mgranada3
▴ 30
0
votes
1
reply
164
views
perseus software (version 1.5.5)
preseus
mass
spectrometry
data
updated 1 day ago by
DGTool
▴ 20 • written 2 days ago by
iqra
• 0
0
votes
1
reply
148
views
Seurat v5 and how to correctly integrate across multiple experiments
Seurat
scRNA
R
updated 1 day ago by
Papyrus
★ 2.9k • written 2 days ago by
yura.grabovska
▴ 90
0
votes
1
reply
149
views
Difference in number of reads when using duplex and simplex base calling with Dorado
base
calling
nanopore
simplex
dorado
duplex
updated 1 day ago by
GenoMax
142k • written 2 days ago by
Lélé
▴ 10
0
votes
1
reply
139
views
How can I calculate the OS of each patient?
overall-survival
updated 1 day ago by
ATpoint
82k • written 1 day ago by
Pedro
• 0
1
vote
1
reply
184
views
Help with VG Toolkit: VCF Output is Empty
vg
updated 1 day ago by
Jordan M Eizenga
▴ 460 • written 11 days ago by
sarumonsus
▴ 10
1
vote
1
reply
146
views
API kegg - IndexError: list index out of range
kegg
API
updated 17 hours ago by
Nyksubuz
▴ 20 • written 1 day ago by
mirwa.zidi93
• 0
0
votes
1
reply
136
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
updated 15 hours ago by
Nyksubuz
▴ 20 • written 1 day ago by
Luqman
• 0
0
votes
1
reply
177
views
solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* error: could not open input file /geneInfo.tab #2142
STAR
updated 10 hours ago by
GenoMax
142k • written 18 hours ago by
huxiangyulove
• 0
0
votes
1
reply
92
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
updated 10 hours ago by
dthorbur
★ 2.0k • written 11 hours ago by
Umer
▴ 50
78 results • Page
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Recent Replies
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
Comment: Reconstruction of locus, order contigs
by
dthorbur
★ 2.0k
[Here](https://www.biostars.org/p/9544689/) is a forum post that may answer your question.
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ashkan
▴ 160
@atpoint I checked all transcripts of GAPDH. they all have 0 TPM.
Comment: how to treat the replicates while performing WGCNA
by
andres.firrincieli
3.6k
> 1) I do not want to merge the MEs rather I asked about replicates, as > some replicates of same sample are showing different behavior for…
Comment: How to systematically check if a bam file is truncated
by
alanh
▴ 170
For more details about what `samtools quickcheck` actually checks for, add a few `-v`'s to the command line. $ samtools quickcheck -…
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by
Zhenyu Zhang
★ 1.2k
Second what is said above, ensembl_id is the unique identifier. As a good bioinformatics habit, always use unique identifier for your anal…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
It doesn't work. The annotation labels are still in a default fontsize. I cant find a way to set the fontsize.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
Ram
43k
Yes. The solution to most things with ComplexHeatmap is to play around with parameters.
Comment: Reconstruction of locus, order contigs
by
BATMAN
• 0
I do not want to re-annotate the genome. I ask if there is a way to extract the region aligned with the mauve, in .gbk format.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
Thank you. What exactly do you mean? Changing `ha = rowAnnotation(text = anno_mark(at = mark_at, labels = gene_names_interesting_in_cluster…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
Ram
43k
Try tweaking the `gp` of the rowAnnotation instead of tweaking the `annotation_name_gp` - that might do the trick.
Comment: Help! Reconstruction of locus, order contigs
by
dthorbur
★ 2.0k
I don't understand your comment. What do you mean? > my idea is not to have to write it down If you have an alignment already, why can't…
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by
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6.6k
Hi Lorenzo, That is correct. The initial version of salmon used the RapMap index explained above. When we published the selective align…
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