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1,000 results • Page 3 of 20
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0
votes
8
replies
518
views
STAR aligner options
STAR
27 days ago by theophile • 0
7
votes
8
replies
659
views
6 follow
How to BLAST more than 5 sequences against UniProt database?
BLAST Protein UniProt
19 days ago by Riq ▴ 50
3
votes
8
replies
4.9k
views
An idea to identify batch effects
microarray batch-effect
updated 6 days ago by 43k • written 9.7 years ago by • 0
0
votes
8
replies
5.3k
views
8 follow
cellranger mkref failed
next-gen-sequencing software-error RNA-seq
updated 14 days ago by • 0 • written 4.7 years ago by ▴ 180
0
votes
8
replies
271
views
Error in cnetplot enrichplot package
R
updated 1 day ago by 43k • written 2 days ago by • 0
3
votes
8
replies
1.2k
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq Cellranger STARsolo 10X
updated 4 days ago by 14k • written 9 months ago by ▴ 80
6
votes
8
replies
2.1k
views
Simple explanation and usage of WGCNA package?
wgcna RNA-Seq ChIP-Seq
updated 16 days ago by • 0 • written 3.9 years ago by ▴ 120
17
votes
8
replies
12k
views
9 follow
MAF vs VAF
sequencing
updated 21 days ago by ▴ 80 • written 6.1 years ago by ▴ 50
1
vote
8
replies
3.4k
views
Best way to address different batches of RNA-seq
sequence RNA-Seq RPKM Fold-Change batch-effect
updated 7 days ago by 43k • written 7.0 years ago by ▴ 20
3
votes
8
replies
4.1k
views
Using FPKM and TPM values for batch correction for Single Cell RNA-Seq
fpkm scRNA-seq RNA-Seq tpm batch-effect
updated 6 days ago by 43k • written 4.6 years ago by ▴ 180
7
votes
8
replies
647
views
Why are the basics so complicated? Basic coverage filtering for VCF files
filter vcf coverage
updated 12 days ago by ▴ 40 • written 15 days ago by ▴ 40
5
votes
8
replies
2.3k
views
VariantCalling with single sanger read
snps blast indel Variant-Calling
updated 29 days ago by 43k • written 7.7 years ago by ▴ 70
9
votes
8
replies
5.6k
views
7 follow
CONTRA for CNV detection. troubleshooting
genome next-gen-sequencing cnv software-error
updated 27 days ago by 43k • written 9.9 years ago by ▴ 870
1
vote
8
replies
3.3k
views
cutadapt error problem
next-gen cutadapt
updated 27 days ago by 43k • written 5.6 years ago by ▴ 20
7
votes
7
replies
1.1k
views
Forum: Bioinformatician who was retaliated against after reporting discriminatory harassment - Please help me navigate getting out of the situation I'm in
Career advice
updated 9 days ago by ★ 2.5k • written 9 days ago by • 0
1
vote
7
replies
886
views
GATK Mutect2 Input files reference and features have incompatible contigs: No overlapping contigs found.
hg19 Mutect2 GATK Variant-Calling
updated 29 days ago by 43k • written 9 months ago by ▴ 100
1
vote
7
replies
15k
views
7 follow
How To Annotate Methylation 450K?
methylation
updated 20 days ago by • 0 • written 10.1 years ago by ▴ 210
1
vote
7
replies
427
views
fastp - can I trim specific adapters only?
trimming fastp adapter
13 days ago by liorglic ★ 1.4k
7
votes
7
replies
538
views
Can you suggest a protein PDB that has two chainst but only 50 total number of atoms?
protein pdb protein-databank
updated 12 days ago by 4.5k • written 12 days ago by • 0
4
votes
7
replies
589
views
UK biobank versus Genomics England
WGS DRAGEN GenomicsEngland UK-BRAP vcf
written 12 weeks ago by ★ 4.3k
0
votes
7
replies
1.9k
views
Batch effect correction in RNASeq data and plot Dendrograms cluster
clustering dendrogram RNA-Seq batch-effect
updated 6 days ago by 43k • written 4.0 years ago by ▴ 500
0
votes
7
replies
6.0k
views
Pre-processing of RNA-Seq data for WGCNA
RNA-Seq WGCNA removeBatchEffect DESeq2
updated 7 days ago by 43k • written 7.6 years ago by ▴ 70
4
votes
7
replies
538
views
DESeq2 Multifactor Design
RNA-seq DESeq2
updated 10 days ago by 43k • written 11 days ago by ▴ 20
0
votes
7
replies
642
views
Help with summarizeOverlaps function in RNASeq analysis using R
R RNA-Seq summarizeOverlaps GenomicAlignments
updated 17 days ago by ★ 1.7k • written 25 days ago by • 0
0
votes
7
replies
396
views
DESeq: too low p-value for RNAseq
R DESeq p-value RNA-seq FDR
updated 19 days ago by ★ 2.9k • written 20 days ago by ▴ 10
2
votes
7
replies
504
views
STARsolo ; Reads are NOT mapped to transcriptome
STARsolo
updated 13 days ago by 141k • written 15 days ago by • 0
3
votes
7
replies
957
views
How much adapters is it ok to keep in my samples after RNA seq?
RNA-seq illumina adapters
updated 20 days ago by 43k • written 5 months ago by ▴ 150
10
votes
7
replies
7.1k
views
6 follow
Convert GVF to VCF
vcf
updated 8 days ago by • 0 • written 9.2 years ago by ▴ 970
4
votes
7
replies
2.4k
views
Batch effects vs biological variables
Batch-effect DESeq2 combat_seq
updated 16 days ago by 43k • written 3.7 years ago by ▴ 20
1
vote
7
replies
5.1k
views
How do I plot several sns.clustermap heatmaps in a single figure?
python seaborn
updated 13 days ago by ▴ 40 • written 3.4 years ago by ▴ 880
2
votes
7
replies
5.1k
views
9 follow
problem with HOMER findMotifsGenome.pl
HOMER ATAC-Seq
updated 13 days ago by • 0 • written 5.5 years ago by ▴ 80
0
votes
7
replies
471
views
Selection criteria for nanobody
Nanobody
updated 23 days ago by 3.9k • written 23 days ago by • 0
2
votes
7
replies
5.2k
views
6 follow
Memory usage of picard Samsort
Picard SortSam
updated 5 days ago by 82k • written 7.1 years ago by ▴ 80
3
votes
7
replies
441
views
Integration of transcriptomics and proteomics: difficult matching names
rna-seq tmt nomenclature proteomics
8 days ago by ntsopoul ▴ 60
7
votes
7
replies
1.0k
views
Prediction tools summary - zero values
statistics
updated 7 days ago by • 0 • written 6 months ago by ▴ 50
3
votes
7
replies
513
views
Artificial deletion in bam
bam
updated 19 days ago by ★ 1.2k • written 20 days ago by ▴ 10
6
votes
7
replies
1.6k
views
How to assess RNA-Seq batch correction success?
Combat RNA-Seq Limma DESeq2 batch-effect
updated 6 days ago by 43k • written 4.9 years ago by ▴ 140
1
vote
7
replies
456
views
Installing Cell Ranger
cellranger
22 days ago by gdfsnkfns • 0
3
votes
7
replies
574
views
Blast NCBI online using R
R NCBI BLAST Rstudio
29 days ago by Begonia_pavonina ▴ 150
4
votes
7
replies
557
views
Can any JBrowse2 tracks show multiple colors for reads at different nucleotide positions?
JBrowse JBrowse2
updated 22 days ago by ★ 3.8k • written 26 days ago by ▴ 140
5
votes
7
replies
2.7k
views
DESeq2 for differential gene expression on GTEx dataset
differential-gene-expression RNA-Seq GTex DESeq2
updated 15 days ago by 43k • written 6.4 years ago by ▴ 10
2
votes
7
replies
665
views
Selecting query format for repeated calls to NCBI's API
NCBI esummary elink API efetch
updated 29 days ago by 141k • written 9 weeks ago by 4.2k
2
votes
7
replies
802
views
Removing duplicates
duplicates ONT minimap2
updated 5 days ago by ▴ 510 • written 7 days ago by • 0
4
votes
7
replies
4.5k
views
snakemake output directory
snakemake ngs
updated 8 days ago by • 0 • written 3.9 years ago by ▴ 200
3
votes
7
replies
1.0k
views
Can I use batch effect correction "by parts"?
ComBat RNA-Seq batch-effect
updated 7 days ago by 43k • written 4.3 years ago by ▴ 360
0
votes
7
replies
410
views
Salmon Quantification in Alignment based-mode
Salmon RNA-seq TPM
updated 27 days ago by 141k • written 28 days ago by • 0
2
votes
7
replies
5.7k
views
8 follow
How to access specifically 30x NA12878 sequencing runs
giab benchmark fastq wgs data-access
updated 22 days ago by ▴ 360 • written 5.1 years ago by • 0
15
votes
6
replies
1.3k
views
6 follow
VCF to human friendly form?
vcf visualization
updated 9 days ago by 161k • written 19 months ago by ▴ 10
0
votes
6
replies
452
views
Error in running Mauve alignner in Ubuntu 20.04
java linux aligner mauve
14 days ago by marongiu.luigi ▴ 710
4
votes
6
replies
440
views
Odd results with BLAST remote
blast remote NCBI
updated 8 days ago by ▴ 170 • written 9 days ago by ▴ 150
1,000 results • Page 3 of 20
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Comment: PCA plot (Suggestions Needed)
Answer: PCA plot (Suggestions Needed)
PCA plot (Suggestions Needed)
Comment: To get p-values for the TPM
A: Where To Download Pam50 Gene Set?
A: Where To Download Pam50 Gene Set?
Answer: Fail to install umap-learn in R
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Recent Replies
Comment: Creating Synthetic Sequences for a ML Model by biochugs • 0
Thanks for the input. I'll continue to think of more ideas that may be achievable.
Comment: PCA plot (Suggestions Needed) by Jeremy ▴ 890
You could also try kernel PCA, which is a non-linear form of PCA, although this will be more time-consuming.
Comment: Troubleshooting RNA-seq data with DNA contamination by DKA ▴ 40
I have unstranded RNA-seq data. Please share the tool with me, if you do not mind.
Comment: PCA plot (Suggestions Needed) by Mensur Dlakic ★ 27k
Everything that @f1f58aed said, plus that there may be no data manipulation that will give you the clusters you expected. Sometimes there a…
Answer: Creating Synthetic Sequences for a ML Model by Mensur Dlakic ★ 27k
It is a good idea, though I don't see how it would work in practice. I think you will encounter at least additional problem on top of da…
Answer: PCA plot (Suggestions Needed) by Jeremy ▴ 890
Right now, the WT samples are clustering together, but you have one mutant sample off by itself, which could be an outlier. How did you sc…
Comment: Adding CB tag to bam file by GenoMax 141k
@yokofakun had written this: https://www.biostars.org/p/336965/ https://github.com/ruqianl/appendCB may also be useful.
Comment: Troubleshooting RNA-seq data with DNA contamination by GenoMax 141k
Please post information about your tool as a `tools` category post. Don't wait/ask other users to ask you.
Comment: Adding CB tag to bam file by Maria • 0
Sorry for the delay in my answer, I got sidetracked. I am using ```samtools addreplacerg -r "@RG\tID:$cell" -o $cell.bam -h $LINE``` bu…
Answer: Troubleshooting RNA-seq data with DNA contamination by haibol2017 ▴ 10
We just developed a R package to tackle this problem. Do you have stranded or unstranded RNA-seq data contaminated with gDNA? If you wou…
Comment: How to trim transcripts using information from NCBI contamination screen report by GenoMax 141k
`bbduk.sh` can use the transcripts as input. There is a `adapters.fa` included in the `resources` directory of the distribution. You can do…
Comment: PCA plot (Suggestions Needed) by swbarnes2 14k
Cross posted here (including the code used to make up the counts): https://support.bioconductor.org/p/9157911/#9157959
Comment: To get p-values for the TPM by swbarnes2 14k
RSEM returns a kind of p-value if you run it with the "prior-enhanced" option. Did you do that? Are you completely sure that's the value y…
Comment: How to trim transcripts using information from NCBI contamination screen report by Lada ▴ 30
i checked both of these programs (`bbduk` and `fastp`) and it seems they use reads as inputs (fastq formats)... how can I trim my transcrip…
Comment: AGeNT LocatIt by barslmn ★ 2.1k
He is already giving 32G, 320G for marking duplicates for exome is excessive. Is there a specific reason for using the tool?
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