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189 results • Page 2 of 4
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4
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355
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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
3
votes
4
replies
411
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR masspec uORF peptide
updated 3 days ago by 142k • written 3 days ago by 161k
1
vote
4
replies
298
views
Add stats to boxplot in R
stats R
4 days ago by Ghada • 0
2
votes
4
replies
310
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq vcf variant-calling
4 days ago by Esraa • 0
1
vote
4
replies
353
views
Contig assembly task, errors
dna genetics contig assembly
updated 6 days ago by 43k • written 11 days ago by • 0
2
votes
4
replies
275
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell seurat 10XGenomics scRNAseq
updated 4 days ago by ▴ 90 • written 4 days ago by ▴ 20
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
3
votes
4
replies
335
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq patch freeze genome
updated 2 days ago by 22k • written 3 days ago by • 0
3
votes
3
replies
368
views
Kraken2 database
kraken microbialdb database krakendb kraken2
updated 6 days ago by ▴ 140 • written 9 days 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
2
votes
3
replies
217
views
RSeQC : infer_experiment.py Error: Could not retrieve index file
RSeQC RNA-Seq
updated 5 days ago by 43k • written 5 days ago by • 0
3
votes
3
replies
234
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm ChIP-seq consensus peaks
updated 3 days ago by 82k • written 4 days ago by • 0
3
votes
3
replies
250
views
getting exon coordinates
genomics
updated 3 days ago by 43k • written 3 days ago by • 0
0
votes
3
replies
358
views
Snakemake wrapper issue
fastqc snakemake
updated 5 days ago by • 0 • written 9 weeks ago by • 0
1
vote
3
replies
285
views
Tool: Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Minutes Decimal offtopic Degrees python
updated 3 days ago by 43k • written 4 days ago by ▴ 30
1
vote
3
replies
208
views
Genotyping sites with N in reference genome
GATK UnifiedGenotyper
updated 4 days ago by ★ 1.2k • written 4 days ago by ▴ 50
1
vote
3
replies
451
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE BAM SAM flag paired-end
6 days ago by kalavattam ▴ 190
2
votes
3
replies
291
views
error in fun(x((i)), ...) : only defined on a data frame with all numeric alike variables
studio Cibersort R
6 days ago by Azra ▴ 10
0
votes
3
replies
373
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified.
DESeq2
6 days ago by mropri ▴ 150
0
votes
3
replies
199
views
Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log10P value
Seurat single-cell scRNA-seq R
updated 6 days ago by 43k • written 6 days ago by • 0
1
vote
3
replies
803
views
About runing Pilon on individual chromosomes when polish draft genome assembly
Pilon chromosome polish genome draft
updated 3 days ago by ▴ 90 • written 2.7 years ago by ▴ 80
1
vote
3
replies
282
views
Is there any way to modify this pie chart ?
pie ggplot R chart
updated 3 days ago by 142k • written 6 days ago by ▴ 40
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
220
views
Biomart issue, why so few 3'utrs?
utr biomart
updated 5 days ago by 142k • written 6 days ago by ▴ 270
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
1
vote
3
replies
294
views
Using ggplotly in R
ggplot ggplotly
updated 4 days ago by ★ 16k • written 5 days ago by ▴ 10
2
votes
3
replies
289
views
Finding variants within a subset of a BAM file
variant calling
5 days ago by ramiro.barrantes • 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
2
votes
3
replies
253
views
ggrepel function: geom_text_repel()
ggplot2 ggrepel R
updated 3 days ago by 43k • written 4 days ago by ▴ 20
0
votes
3
replies
268
views
RNAseq RNA content
mRNA Linux rRNA RNA-seq RNA
updated 5 days ago by ▴ 580 • written 5 days ago by ▴ 10
1
vote
2
replies
269
views
How to interpret infinite odds ratio?
statistics
5 days ago by Lukas • 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
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
4
votes
2
replies
195
views
Duplicated sequence samtools
bowtie2 samtools
updated 6 days ago by 142k • written 6 days ago by • 0
0
votes
2
replies
441
views
News: FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last places available
DNA-seq variant-calling RNA-seq illumina transcriptomics
6 days ago by David Langenberger 11k
1
vote
2
replies
1.3k
views
Extracting named fasta sequences according to list with Biopython
Biopython FASTA
updated 6 days ago by • 0 • written 2.6 years ago by • 0
3
votes
2
replies
289
views
imputation through beagle
panel beagle reference imputation
5 days ago by analyst ▴ 50
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
2
votes
2
replies
208
views
Genome Visualization Tools
bacterial genome
updated 5 days ago by 142k • written 5 days ago by ▴ 10
1
vote
2
replies
213
views
Alphafold 3 pLDDT coloring scheme in chimerax?
ChimeraX Alphaphold Alphaphold3
updated 4 days ago by 6.4k • written 5 days ago by • 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
2
votes
2
replies
205
views
genome finishing
finishing genome
updated 4 days ago by ▴ 20 • written 4 days ago by • 0
1
vote
2
replies
235
views
Doubt about the process of annotation, detection, identification and classification of transposable elements
annotation TransposableElements
4 days ago by MarcosCosta • 0
0
votes
2
replies
231
views
Inquiry about deseq2 transformation
RNA-seq deseq2
4 days ago by Chen • 0
2
votes
2
replies
192
views
Cannot install bwa-mem2 via conda
conda mamba python
updated 3 days ago by 43k • written 4 days ago by • 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
270
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
237
views
How to generate table_annovar from VCF input?
vcf annovar
updated 2 days ago by 161k • written 3 days ago by ▴ 70
189 results • Page 2 of 4
Recent Votes
A: How To Split One Big Sequence File Into Multiple Files With Less Than 1000 Seque
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
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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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