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801 results • Page 4 of 17
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3
votes
8
replies
1.4k
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq Cellranger STARsolo 10X
updated 27 days ago by 14k • written 9 months ago by ▴ 80
3
votes
0
replies
239
views
News: Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Scanpy Generative-AI scRNA Machine-Learning
updated 20 days ago by 43k • written 21 days ago by ▴ 60
3
votes
4
replies
744
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
24 days ago by rahu • 0
3
votes
9
replies
941
views
How can I retrieve wheat lysine non-acetylated sequences from the UniProt database?
UniProt
updated 28 days ago by ★ 2.4k • written 29 days ago by • 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 82k • written 4 days ago by • 0
3
votes
4
replies
333
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR masspec uORF peptide
updated 20 hours ago by 142k • written 1 day ago by 161k
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk genomicsdbimport
updated 14 days ago by • 0 • written 5.1 years ago by 11k
3
votes
2
replies
420
views
Extract protein sequence
fasta alignment blast
16 days ago by anna ▴ 20
2
votes
6
replies
5.3k
views
How to avoid over-correction by using harmony or CCA to batch correction in scRNA-seq?
scRNA-seq R seurat harmony batch-effect
updated 28 days ago by 43k • written 3.8 years ago by • 0
2
votes
1
reply
332
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
updated 13 days ago by 10k • written 17 days ago by ▴ 10
2
votes
2
replies
348
views
Association study using SNP data
Association Allele Parentage SNP
11 days ago by drajangirija • 0
2
votes
5
replies
638
views
MEGA Analysis Issue on High-Performance Computer
phylogenetic-analysis MEGA
updated 26 days ago by ★ 27k • written 27 days ago by • 0
2
votes
1
reply
148
views
java out of memory error through beagle for imutation
beagle java.out.of.memory imputation
9 days ago by analyst ▴ 50
2
votes
4
replies
1.4k
views
How to fix Error in dat[, batch == batch_level] : (subscript) logical subscript too long when removing batch effects
microarray combat batch-effect median-normalization
updated 28 days ago by 43k • written 18 months ago by • 0
2
votes
3
replies
208
views
RSeQC : infer_experiment.py Error: Could not retrieve index file
RSeQC RNA-Seq
updated 2 days ago by 43k • written 2 days ago by • 0
2
votes
4
replies
272
views
Where to get the following bed file?
WES bed reference file
updated 10 days ago by 142k • written 10 days ago by • 0
2
votes
1
reply
297
views
Pediococcus acidilactici sequence analysis
BLAST Gene-Ontology
updated 29 days ago by 43k • written 29 days ago by ▴ 120
2
votes
5
replies
10k
views
Find Corresponding Author: Doi Metadata?
updated 25 days ago by 43k • written 10.6 years ago by ▴ 150
2
votes
9
replies
938
views
TCGA2STAT Error: Firehose connection
FIREHOSE TCGA
updated 23 days ago by 4.2k • written 7 months ago by • 0
2
votes
3
replies
335
views
Problem with Seurat package in PercentageFeatureSet function
cell single
updated 7 days ago by ★ 2.5k • written 12 days ago by ▴ 60
2
votes
2
replies
1.6k
views
Combining control samples from 2 separate studies. Model matrix for batch effect?
gene-expression R limma batch-effect model-matrix
updated 28 days ago by 43k • written 7.3 years ago by ▴ 20
2
votes
2
replies
250
views
STRING-DB API can't find my protein but I can find it when I go to the STRING-DB website directly
STRING-DB protein STRING-DB-API
11 days ago by brandon • 0
2
votes
4
replies
292
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq vcf variant-calling
2 days ago by Esraa • 0
2
votes
5
replies
423
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq assembly transcriptome contamination
21 days ago by Lada ▴ 30
2
votes
1
reply
232
views
Failed to open VCF file
GATK sentieon BWA-MEM
updated 5 days ago by 161k • written 6 days ago by ▴ 70
2
votes
2
replies
189
views
Is therer any suggestions on mapping rate of WGBS data?
mapping read alignment WGBS
9 days ago by Zeng Jingyu ▴ 60
2
votes
3
replies
500
views
Sheep reference genome remapping coordinates
reference remap sheep coordinates genome
28 days ago by valentinatsar • 0
2
votes
4
replies
2.7k
views
When to use .vcf or .gvcf files from GATK HaplotypeCaller?
indel gatk calling snp variant
updated 17 days ago by 9.7k • written 2.0 years ago by ▴ 120
2
votes
3
replies
272
views
Finding variants within a subset of a BAM file
variant calling
2 days ago by ramiro.barrantes • 0
2
votes
4
replies
719
views
Count all variants from vcf file
variants vcf Count
updated 10 days ago by 161k • written 21 months ago by • 0
2
votes
5
replies
538
views
Fetch table from clinvar database according to a list of rsid
python clinvar perl
18 days ago by ashaneev07 ▴ 20
2
votes
3
replies
322
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus annotation assembly genome
updated 13 days ago by ★ 2.0k • written 14 days ago by ▴ 30
2
votes
1
reply
258
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome PHG graph
updated 4 days ago by ▴ 210 • written 6 days ago by ▴ 10
2
votes
2
replies
180
views
Cannot install bwa-mem2 via conda
conda mamba python
updated 19 hours ago by 43k • written 1 day ago by • 0
2
votes
5
replies
404
views
Importing a fastq file
Fastq
updated 7 days ago by ▴ 120 • written 8 days ago by • 0
2
votes
3
replies
390
views
How to establish haplotype-specific gene expression levels
RNA-seq Haplotype
updated 20 days ago by ★ 6.0k • written 5 weeks ago by ▴ 60
2
votes
5
replies
567
views
Tissue-specific DEG analysis with DEseq2
DEseq2 RNA-seq DEG R
updated 4 days ago by ▴ 40 • written 13 days ago by ▴ 30
2
votes
7
replies
1.4k
views
6 follow
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq Salmon Isoseq
updated 18 days ago by ★ 7.2k • written 8 months ago by ▴ 10
2
votes
4
replies
2.4k
views
How could I generate a gi_taxid_nucl.dmp file similar to the one previously hosted by NCBI?
ncbi metagenomics centrifuge gi_taxid_nucl.dmp taxonomy
updated 22 days ago by • 0 • written 2.5 years ago by • 0
2
votes
4
replies
389
views
Should I use unpaired reads from trimmomatic
RNA-seq QC Trimmomatic
updated 23 days ago by 14k • written 24 days ago by • 0
2
votes
3
replies
995
views
Method to detect genome doubling
CNV genome doubling
updated 24 days ago by 4.2k • written 4.5 years ago by ▴ 750
2
votes
4
replies
4.5k
views
Differential Expression Analysis with monocle and batch effect correction
single-cell RNA-Seq batch-effect
updated 29 days ago by 43k • written 6.0 years ago by ▴ 60
2
votes
1
reply
2.1k
views
How to make batch univariate cox analysis for list
univariate-cox-analysis
updated 28 days ago by 43k • written 4.8 years ago by ▴ 20
2
votes
2
replies
311
views
p-value in CIBERSORT
CIBERSORT p-value
16 days ago by michelafrancesconi9 ▴ 20
2
votes
5
replies
535
views
Marking duplicates using UMIs
Deduplication UMI
updated 25 days ago by 19k • written 26 days ago by • 0
2
votes
6
replies
3.8k
views
Treatment VS Control in Single Cell RNAseq analysis
Single Cell RNAseq DE Analysis Treatment Control
updated 21 days ago by 82k • written 3.9 years ago by ▴ 280
2
votes
0
replies
165
views
Herald: The Biostar Herald for Monday, May 06, 2024
herald
10 days ago by Biostar 2.8k
2
votes
3
replies
844
views
Issues with Mixture file when using CIBERSORTx
Deconvolution CIBERSORTx
updated 12 days ago by • 0 • written 7 months ago by • 0
2
votes
6
replies
380
views
BWA alignment
Samtools bam
updated 2 days ago by ▴ 260 • written 4 days ago by • 0
2
votes
3
replies
195
views
ggrepel function: geom_text_repel()
ggplot2 ggrepel R
updated 11 hours ago by 43k • written 1 day ago by ▴ 20
801 results • Page 4 of 17
Recent Votes
Answer: Generating consensus sequence from bam file
Answer: Short Read Data Genome Assembly
Comment: API kegg - IndexError: list index out of range
Comment: How does FindNeighbors() and FindClusters() related and work?
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
lncRNA and ncPEPs identification
Answer: Identifying common DEGs among multiple datasets
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Recent Replies
Answer: How to handle duplicated genes in TCGA data? by txema.heredia ▴ 130
Having duplicate gene symbols is pretty common. Why do you need to work with gene symbols? To compare them to external datasets? Or just fo…
Comment: Merge clusters in Seurat UMAP by kilcdincer ▴ 10
It did not help either. But I got the answer [here][1] Thank you! [1]: https://github.com/satijalab/seurat/issues/8902
Comment: How to generate table_annovar from VCF input? by Pierre Lindenbaum 161k
there is no `--allsample` option in the "usage" screen you're showing. I suspect you're using an old version ?
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i by egascon • 0
Thank you very much again. I have learned a lot of things.
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i by egascon • 0
It's a microarryay experiment, not RNASeq
Comment: Sam file Header problem by Pierre Lindenbaum 161k
https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups
Answer: Faster Needleman-Wunsch rapid global alignment of two sequences? by DGTool ▴ 20
I have also recently come across another global alignment algorithm that was recently released which could seem pretty interesting to test …
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by b.contreras.moreira ▴ 190
Not sure, you might ask in the repo, please share here the response if you find it
Comment: How to generate table_annovar from VCF input? by LucisTheFather • 0
Would you be more specific to your question? Do you mean how to debug this syntax error?
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by hophuquy0944 • 0
thank you
Comment: How to extract cells of different species after mapping with combined genome? by Tony • 0
I think this method should be applicable to all high-throughput single-cell RNA-seq platforms. Although the method of determining cell spec…
Comment: BiomartException: Query ERROR for existing dataset in BioMart by Nyksubuz ▴ 20
The dataset you want (taestivum_eg_gene) exists within the "plants_mart" schema, not the default schema. Your current code assumes the defa…
Comment: Add line under stat test by Nyksubuz ▴ 20
You could use [this][1] [1]: https://ggplot2.tidyverse.org/reference/geom_segment.html
Comment: API kegg - IndexError: list index out of range by Nyksubuz ▴ 20
It might be because the gene symbol is not found in the KEGG database. Add some extra error handling before parsing the results or do a man…
Comment: Sam file Header problem by saifulislam99121 • 0
Thank you for your reply. I am not very much sure about this RG. Can you explain me a bit?
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