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1,000 results • Page 5 of 20
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1
vote
5
replies
1.0k
views
Align short sequence against ONT reads
long-reads ONT alignment genome
updated 19 days ago by 43k • written 22 months ago by ▴ 40
0
votes
5
replies
872
views
extraction of spanning long reads
long-reads
updated 19 days ago by 43k • written 17 months ago by ▴ 110
0
votes
5
replies
1.8k
views
Demultiplexing multiple amplicons from one fastq based on primer sequence
demultiplexing illumina
updated 15 days ago by 3.2k • written 3.4 years ago by • 0
0
votes
5
replies
372
views
Parsing fasta file by coordinates
linux fasta
updated 27 days ago by 141k • written 29 days ago by ▴ 120
2
votes
5
replies
1.9k
views
Differential Expression Analysis with batches which have different biological groups
R RNA-Seq limma DE batch-effect
updated 7 days ago by 43k • written 4.8 years ago by ▴ 60
3
votes
5
replies
2.1k
views
DE analysis with edgeR and possibly batch effect
analysis edgeR batch-effect DE
updated 7 days ago by 43k • written 5.1 years ago by ★ 1.9k
3
votes
5
replies
1.3k
views
NextGen Sequencing Folks, what do you keep as your raw backup? BCL's or FASTQ's? Both?
next-gen-sequencing backups data-storage
updated 19 days ago by 43k • written 2.1 years ago by ▴ 130
0
votes
5
replies
339
views
calculate mismatch rate from VCF file
mismatch-rate VCF
updated 27 days ago by 43k • written 27 days ago by ▴ 10
0
votes
5
replies
252
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap alignment minimap2 GRCh38 assembly
8 hours ago by njornet ▴ 20
3
votes
5
replies
1.3k
views
How to identify antibiotic resistant genes in gene databases?
antibiotic Gene-Ontology GO
updated 13 days ago by 43k • written 2.0 years ago by • 0
0
votes
5
replies
322
views
BUSCO analysis failed due to Duplicate of sequence in Input genome fasta. How to solve this problem ?
duplicate BUSCO.
updated 20 days ago by 141k • written 20 days ago by ▴ 10
3
votes
5
replies
461
views
Having trouble building VG in Ubuntu
vg
updated 10 days ago by 43k • written 13 days ago by • 0
2
votes
5
replies
422
views
Marking duplicates using UMIs
Deduplication UMI
updated 2 days ago by 19k • written 3 days ago by • 0
1
vote
5
replies
1.5k
views
How to correct unknown Batch effect?
PCA gene-expression DESeq2 RNA-seq batch-effect
updated 7 days ago by 43k • written 12 months ago by ▴ 110
5
votes
5
replies
533
views
NCBI MEGABLAST versus UCSC BLAT
blast blat alignment megablast
updated 14 days ago by ▴ 510 • written 16 days ago by ▴ 40
0
votes
5
replies
5.9k
views
Calculate Radius of Gyration [python 3]
biopython PDB Radius of Gyration python protein
updated 4 days ago by • 0 • written 6.5 years ago by ▴ 30
2
votes
5
replies
425
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats hg002 bed homopolymer-regions
7 days ago by Bikram Kumar • 0
9
votes
5
replies
2.2k
views
Millions of Reads Needed for Differential Gene Expression
differential-gene-expression RNA-Seq deseq2
updated 15 days ago by 43k • written 4.6 years ago by ▴ 20
2
votes
5
replies
350
views
WGCNA website
wgcna
updated 18 days ago by 141k • written 20 days ago by ★ 1.7k
1
vote
5
replies
334
views
samtools filtering
samtools
updated 13 days ago by ★ 1.2k • written 20 days ago by ▴ 80
2
votes
5
replies
2.3k
views
DGE on transcriptomic data, focus on transcript sequences or in derivated ORFs?
differential-gene-expression RNA-Seq ORFs
updated 15 days ago by 43k • written 6.4 years ago by ▴ 90
1
vote
5
replies
402
views
Need information on how filterAndTrim function from the DADA2 pipeline was developed
filterAndTrim dada2
updated 19 days ago by 141k • written 20 days ago by • 0
2
votes
5
replies
994
views
Ties in reranked list
fgsea GSEA
updated 11 days ago by • 0 • written 7 months ago by • 0
2
votes
5
replies
667
views
samtools mpileup taking too long
Bam samtools sam alignment
updated 19 days ago by 43k • written 6 weeks ago by • 0
1
vote
5
replies
582
views
Cell barcode whitelists for DNBelab C Series High-throughput Single-cell RNA Series Library Preparation Set?
cell-barcode MGI DNBelab single-cell
updated 1 day ago by • 0 • written 3 months ago by • 0
2
votes
5
replies
504
views
MEGA Analysis Issue on High-Performance Computer
phylogenetic-analysis MEGA
updated 3 days ago by ★ 27k • written 4 days ago by • 0
0
votes
5
replies
412
views
Error running local blastn in R using system2
blastn NCBI R
26 days ago by Harrison • 0
4
votes
5
replies
231
views
To get p-values for the TPM
P-value TPM RSEM
updated 2 hours ago by 14k • written 13 hours ago by • 0
1
vote
5
replies
2.3k
views
Shannon vs Simpson for TCR diversity estimation
TCR shannon simpson
updated 13 days ago by 82k • written 5.0 years ago by ▴ 750
5
votes
5
replies
7.2k
views
Converting scRNA-Seq to Bulk-RNASeq
scRNASeq bulk-RNASeq RNA-Seq single-cell
updated 13 days ago by • 0 • written 3.8 years ago by ★ 1.8k
2
votes
5
replies
2.2k
views
Generating a heatmap in DEG analysis
Differential-gene-expression RNA-Seq
updated 15 days ago by 43k • written 3.1 years ago by ▴ 10
2
votes
5
replies
471
views
Creating an index from multiple .fsa files
HISAT2 BWA Alignment
15 days ago by theworldsagainstme • 0
4
votes
5
replies
1.9k
views
which package should be selected for differential gene expression analysis
Differential-gene-expression RNA-Seq
updated 15 days ago by 43k • written 5.5 years ago by ▴ 100
0
votes
5
replies
520
views
Adding CB tag to bam file
samtools bam
updated 32 minutes ago by 141k • written 5 days ago by • 0
5
votes
5
replies
842
views
Blacklist for bacterial genome [ChIPseq]?
ChIPseq Blacklist
updated 12 days ago by 43k • written 10 months ago by ▴ 30
2
votes
5
replies
2.8k
views
Batch effect in Axiom Human Origins Array
affymetrix array batch-effect
updated 7 days ago by 43k • written 7.9 years ago by ▴ 50
0
votes
5
replies
599
views
How to deeply sequence long inserts
Long-read phage NGS
updated 19 days ago by 43k • written 4 months ago by • 0
2
votes
5
replies
1.9k
views
alignement and Variant calling with BWA and samtools
variant-calling samtools BWA
updated 29 days ago by 43k • written 3.0 years ago by ▴ 30
3
votes
5
replies
652
views
somatic variant calling without matched normal in long-reads
variants cancer illumina ONT nanopore
29 days ago by eesiribloom ▴ 80
3
votes
5
replies
1.8k
views
Limma/edgeR Design matrix for gender effect
RNA-Seq batch-effect
updated 7 days ago by 43k • written 4.7 years ago by • 0
37
votes
5
replies
13k
views
How do you generate TMM normalized counts using EdgeR?
R RNA-seq edgeR
updated 14 days ago by ▴ 60 • written 2.9 years ago by ★ 1.0k
8
votes
5
replies
1.2k
views
Classifying repeat features from Ensembl
ensembl repeat
updated 9 days ago by ▴ 200 • written 16 months ago by ★ 1.4k
2
votes
5
replies
1.0k
views
Why multiple SYMBOLS, Consequences... for Variant Effect Predictor (VEP)
VEP
updated 29 days ago by ★ 2.1k • written 16 months ago by ▴ 80
1
vote
5
replies
364
views
Best way to deal with overlapping read names in merged BAM files
picard MarkDuplicates
9 days ago by shpak.max ▴ 50
0
votes
5
replies
495
views
How to download RNAseq data of only male KIRC patients?
TCGAbiolinks
29 days ago by bioinfo_enthusiast • 0
1
vote
5
replies
2.8k
views
Batch effect identification using PCA
PCA qRT-PCR R targeted-assay Batch-Effect
updated 9 days ago by 43k • written 3.9 years ago by ▴ 250
4
votes
5
replies
346
views
merging tetraploid vcf files through bcftools
vcf bcftools
22 days ago by analyst ▴ 30
0
votes
5
replies
329
views
Incongruencies in GT assignment by Freebayes
depth freebayes heterozygous genotype
19 days ago by virginia.baraja • 0
1
vote
5
replies
236
views
Downsampling fastq file
downsample fastq
updated 2 days ago by 43k • written 2 days ago by ▴ 80
2
votes
5
replies
673
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 3 days ago by ▴ 740 • written 5 days ago by ★ 2.4k
1,000 results • Page 5 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: 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?
Comment: How to convert plink files to Hapmap Format by bk11 ★ 2.3k
This looks good. Please try with using `--allow-no-sex flag` plink --bfile your_data_phenoUP --assoc --allow-no-sex --out your_data_ph…
Comment: How to convert plink files to Hapmap Format by Sofia • 0
SC899359_PC75420_A05 SC899359_PC75420_A05 0 0 0 2 SC899360_PC75415_D01 SC899360_PC75415_D01 0 0 0 2 SC899361_PC75425_H05 SC899361_PC75425_H…
Comment: How to convert plink files to Hapmap Format by bk11 ★ 2.3k
Please show me a few lines of phenotype updated .fam file. You can do `head your_data_phenoUP.fam` and paste result here. Please do not us…
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