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86 results • Page 1 of 2
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1
vote
16
replies
750
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast ncbi
updated 1 day ago by 142k • written 4 days ago by • 0
2
votes
9
replies
1.1k
views
HGVS Nomenclature of Multiple Indels found in Cis
Nomenclature HGVS
13 hours ago by LauferVA 4.2k
0
votes
9
replies
607
views
Using VEP annotation output as the input for a second VEP annotation
Annotation VEP VCF
4 days ago by Arton ▴ 10
5
votes
7
replies
519
views
RNA seq analysis
DESeq RNA-seq
4 days ago by Jacek ▴ 20
0
votes
6
replies
339
views
ComplexHeatmap - How to change fontsize of rowAnnotation
ComplexHeatmap
2 days ago by hannes.bongartz • 0
0
votes
5
replies
290
views
bbmerge (bbmap) ~ error with insert size file output
bbtools bbmerge bbmap
updated 4 days ago by 142k • written 4 days ago by • 0
1
vote
5
replies
350
views
Reconstruction of locus, order contigs
contigs cluster alignment locus
updated 2 days ago by ★ 2.0k • written 3 days ago by • 0
0
votes
5
replies
330
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
6 days ago by SilhouetteQ • 0
0
votes
4
replies
284
views
how to treat the replicates while performing WGCNA
clustering WGCNA replicates
1 day ago by mavy ▴ 10
0
votes
4
replies
329
views
Merge clusters in Seurat UMAP
seurat umap
2 days ago by kilcdincer ▴ 10
1
vote
4
replies
355
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus annotation assembly genome
updated 5 days ago by 8.6k • written 6 days ago by ▴ 30
0
votes
4
replies
268
views
Galaxy StringTie error
stringtie galaxy
5 days ago by trkfs • 0
1
vote
4
replies
329
views
Help with Biopython for Beginner
Python ORF FASTA Biopython
updated 1 day ago by 21k • written 11 days ago by • 0
0
votes
4
replies
408
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
6 days ago by beginner123 • 0
0
votes
4
replies
3.6k
views
SNPEff database building error
SNP
updated 6 days ago by • 0 • written 7.1 years ago by • 0
3
votes
3
replies
295
views
Gene Specific coverage from WGS data
WGS SARS-CoV2
updated 6 days ago by 43k • written 19 days ago by • 0
0
votes
3
replies
171
views
Problem with Calling Variants from RNA-Seq data
vcf gatk benchmark giab rna-seq
4 days ago by Esraa • 0
0
votes
3
replies
211
views
How to access GWAVA software of data
GWAVA
updated 5 days ago by 142k • written 5 days ago by ▴ 10
0
votes
3
replies
280
views
Sam file Header problem
Sam Header problem file
updated 2 days ago by 161k • written 3 days ago by • 0
0
votes
3
replies
357
views
Snakemake wrapper issue
fastqc snakemake
updated 5 days ago by • 0 • written 9 weeks ago by • 0
1
vote
2
replies
366
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 6 days ago by 43k • written 7 days ago by • 0
0
votes
2
replies
236
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated java.nio.bufferunderflowexception haplotypecaller bqsr
6 days ago by analyst ▴ 50
0
votes
2
replies
219
views
Output file of samtools flagstat empty
samtools-flagstat
updated 6 days ago by 6.4k • written 7 days ago by • 0
3
votes
2
replies
203
views
Publish a Letter in higher impact vs Research article in lower impact
Article Letter Journal
updated 6 days ago by 82k • written 6 days ago by • 0
0
votes
2
replies
187
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp filteration genotype quality GATK
5 days ago by IdaHao0921 • 0
0
votes
2
replies
194
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming adapters cutadapt sRNA-seq smallRNA
4 days ago by melissa.joubert • 0
1
vote
2
replies
233
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart RNAseq kallisto
3 days ago by bioinfo ▴ 150
2
votes
2
replies
268
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell ambient-RNA
updated 3 days ago by 43k • written 3 days ago by ▴ 130
0
votes
2
replies
236
views
How to generate table_annovar from VCF input?
vcf annovar
updated 2 days ago by 161k • written 3 days ago by ▴ 70
0
votes
2
replies
302
views
Traveler with Infernal mapping failed
r2dt
updated 1 day ago by • 0 • written 3 months ago by • 0
0
votes
2
replies
215
views
What marks a De-Novo Genome assembly as FAILED?
nanopore denovo illumina assembly genome
12 hours ago by Umer ▴ 50
0
votes
2
replies
185
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart ensembl wheat python pybiomart
1 hour ago by Luqman • 0
0
votes
1
reply
152
views
Seurat v5 and how to correctly integrate across multiple experiments
Seurat scRNA R
updated 3 days ago by ★ 2.9k • written 4 days ago by ▴ 90
1
vote
1
reply
200
views
API kegg - IndexError: list index out of range
kegg API
updated 3 days ago by ▴ 20 • written 3 days ago by • 0
0
votes
1
reply
157
views
Add line under stat test
stats R
updated 3 days ago by ▴ 20 • written 4 days ago by • 0
0
votes
1
reply
145
views
Broad and Narrow peaks
ATAC ChIP seq
updated 1 day ago by 82k • written 1 day ago by ▴ 20
0
votes
1
reply
153
views
Difference in number of reads when using duplex and simplex base calling with Dorado
base calling nanopore simplex dorado duplex
updated 3 days ago by 142k • written 4 days ago by ▴ 10
0
votes
1
reply
152
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences Demuxlet
updated 6 days ago by 43k • written 6 days ago by • 0
1
vote
1
reply
183
views
constructing pangenome through psvcp
psvcp pangenome
1 day ago by analyst ▴ 50
0
votes
1
reply
141
views
Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
annotation vcf vep zygosity deepvariant
4 days ago by asalimih ▴ 60
0
votes
1
reply
210
views
How can I calculate the OS of each patient?
overall-survival
updated 3 days ago by 82k • written 3 days ago by • 0
1
vote
1
reply
296
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx cibersort error RNA-Seq deconvolution
updated 1 day ago by • 0 • written 3 months ago by ▴ 10
0
votes
1
reply
385
views
solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* error: could not open input file /geneInfo.tab #2142
STAR
updated 2 days ago by 142k • written 3 days ago by • 0
0
votes
1
reply
164
views
Can diamond prepdb be used to make a taxonomically aware database?
blast diamond taxonomy
updated 6 days ago by 142k • written 6 days ago by • 0
0
votes
1
reply
165
views
How to process Bulk WES data?
WES WGS
updated 6 days ago by 142k • written 6 days ago by • 0
1
vote
1
reply
149
views
sci-RNA-seq
Seurat sci-RNA-seq
updated 5 days ago by 43k • written 5 days ago by ▴ 10
0
votes
1
reply
165
views
consensus sequence calling
consensus
updated 6 days ago by ★ 2.5k • written 6 days ago by • 0
0
votes
1
reply
175
views
What's next after GATK variant calling pipeline?
GATK pipeline figures DNA-seq
updated 3 days ago by 54k • written 4 days ago by ▴ 30
1
vote
1
reply
192
views
Help with VG Toolkit: VCF Output is Empty
vg
updated 3 days ago by ▴ 460 • written 13 days ago by ▴ 10
0
votes
1
reply
150
views
Polish a large genome with Pilon
Pilon Pacbio Polish Illumina
4 days ago by sansan_96 ▴ 90
86 results • Page 1 of 2
Recent Votes
C: Snakemake vs. Nextflow: strengths and weaknesses
Answer: workflow management system : WDL, CWL, Ruffus, SnakeMake, etc
Sequence alignment on split read event such as inversion, duplication and complex nested events.
ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
Comment: Add stats to the plot
Post-doctoral Position in Alzheimer’s Disease Genetics, ‘Omics, and Biomarkers
The Biostar Handbook. A bioinformatics e-book for beginners.
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Recent Replies
Comment: BiomartException: Query ERROR for existing dataset in BioMart by Luqman • 0
I am using *pybiomart* which has Server inplace of BiomartServer, I used that as per above but still getting the same error. Also, when I a…
Comment: Blastn, need help to increase speed by m13113153781 • 0
mmseq2 is indeed a good acceleration solution, but its index files require ~ 6 T space....
Answer: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from by KHURRAM SHAHZAD • 0
Thank you it works
Answer: Add stats to the plot by Ghada • 0
I think this is what caused the error. we do not have group 1 and 2 in the statistical test results???? ![enter image description here][…
Answer: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data? by Bibi • 0
@atpoint thanks you for your timely response. Can someone else shed light if we can compare the trend of DEGs using the scRNA and Bulk RNA…
Comment: Add stats to the plot by GenoMax 142k
Please use `101010` to format `code` so it is represented in monospace font. I have done this for you now.
Answer: is there a tool to recover corrupted fastq files by Tommaso • 0
You may also want to give a try to **FastqWiper** (https://github.com/mazzalab/fastqwiper)
Comment: Add stats to the plot by Ghada • 0
Thanks. That helpful. I am getting this error data4_test <- data4.ts%>% ungroup() %>% t.test(data =.,value ~ Condition)%>% + …
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data? by ATpoint 82k
I cannot comment here. You are asking why results between two experiments are different. I do not know without seeing the data.
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data? by Bibi • 0
Thank you so much for this insight. I just want to clarify another point here. I have used scRNA seq data from mice mammary epithelial cell…
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File by Pierre Lindenbaum 161k
> Cannot read non-existent file: file:///local/home/User/VCF_Filtering/biostar.code your file doesn't exist, is at the wrong place etc.
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File by ajbarrett98 • 0
Hi Pierre, I am attempting to run this code and am running into this error: (jvar) $ jvarkit vcffilterjdk -f biostar.code Dart_VCF2_Or…
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data? by ATpoint 82k
I cannot give a precise answer, as ML is not my field, but generally, why don't you apply the method to pseudobulks of the exact single-cel…
Answer: geom_bar issue in ggplot2 with xlim() by ATpoint 82k
https://stackoverflow.com/questions/10365167/geom-bar-bars-not-displaying-when-specifying-ylim
Comment: What marks a De-Novo Genome assembly as FAILED? by Umer ▴ 50
Yes. We are sequencing 45 different samples with illumina. 12 of these are also going to be sequenced with Nanopore (for hybrid assembly). …
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