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975 results • Page 2 of 20
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0
votes
5
replies
330
views
Easy way to find out which allele is minor allele from bed file?
plink
updated 3 days ago by 10k • written 3 days ago by ▴ 750
0
votes
1
reply
200
views
visualize GSEA
barplot RNA-seq GSEA enrichment
updated 2 days ago by 43k • written 3 days ago by ▴ 170
0
votes
1
reply
191
views
fastq screen aligner no specified.
BWA Bowtie2 FastqScreen
updated 2 days ago by 142k • written 3 days ago by • 0
0
votes
1
reply
187
views
filtering before dada2
bbduk qiime2 dada2 metagenomic
updated 2 days ago by 43k • written 3 days ago by • 0
0
votes
6
replies
399
views
Differential Expression Analysis using DESeq2 in R
deseq2 R
updated 3 days ago by 14k • written 3 days ago by • 0
0
votes
2
replies
219
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE BAM SAM flag paired-end
11 hours ago by kalavattam ▴ 190
1
vote
3
replies
269
views
TaxID mapping file
annotation blobtools RNAseq decontamination transcriptomes
1 day ago by Lada ▴ 30
1
vote
0
replies
142
views
.lgen file has 3+ different alleles
PLINK lgen ped
updated 19 hours ago by 11k • written 3 days ago by ▴ 10
0
votes
0
replies
136
views
vcf procesing for ML antigen prediction
formats vcf fastaq HLA_imputation HLA_typing
3 days ago by Javier • 0
0
votes
1
reply
228
views
Extracting mutation status from MAF files - TCGA
TCGA maf mutation
updated 2 days ago by • 0 • written 3 days ago by • 0
0
votes
0
replies
129
views
IGV interpretation for ATM gene for chromosome 11 for a deceased partient suspected of having melanoma
genetic Variant predisposition
3 days ago by mikemakaveli1 • 0
2
votes
2
replies
211
views
Raw counts using stringtie
stringtie RNA-seq
updated 3 days ago by 142k • written 3 days ago by • 0
0
votes
0
replies
128
views
Modify plot R mtDNA indel
plot mtDNA R
3 days ago by marco.barr ▴ 90
0
votes
0
replies
263
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot graphical_output GSEA clusterProfiler
3 days ago by NorbertK • 0
2
votes
2
replies
219
views
Analysis of intronic reads included scRNA-seq data
single-cell
updated 2 days ago by 43k • written 3 days ago by ▴ 30
10
votes
10
replies
615
views
High Malat-1 expression in single cell data
single-cell
updated 15 hours ago by ▴ 10 • written 7 days ago by ▴ 30
0
votes
2
replies
240
views
Downloading older version of a tool
Alignment tools
2 days ago by Ruqaiya • 0
0
votes
0
replies
145
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization illumina ngs sequencing
3 days ago by rustykb ▴ 20
1
vote
1
reply
180
views
DSEQ2 analysis
DESEQ2 logfoldchange
updated 2 days ago by 43k • written 3 days ago by • 0
3
votes
5
replies
272
views
Generating mpileup file using samtools
mpileup samtools
updated 3 days ago by 21k • written 3 days ago by • 0
0
votes
5
replies
346
views
6 follow
What purposes can TPM values be used for?
RNA-seq TPM Normalization DESeq2
updated 3 days ago by ▴ 180 • written 4 days ago by • 0
1
vote
3
replies
282
views
Does comparing two different groups to a common third group introduce bias in the analysis?
DESEQ RNAseq
updated 3 days ago by 82k • written 4 days ago by • 0
0
votes
0
replies
135
views
News: Cellosaurus release 49 is available
cell biocuration line database news knowledgebase
3 days ago by Amos Bairoch ▴ 120
2
votes
3
replies
275
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus annotation assembly genome
updated 3 days ago by ★ 1.9k • written 3 days ago by ▴ 30
0
votes
0
replies
144
views
SIngle cell analysis
Seurat scRNA-seq Harmony DoubletFinder Merge
3 days ago by Jeyong • 0
0
votes
2
replies
728
views
homer not configured properly
Homer makeTagDirectory
updated 3 days ago by • 0 • written 23 months ago by • 0
1
vote
3
replies
254
views
Bedtools merge minimum overlap?
bedtools genomics
updated 4 days ago by 35k • written 4 days ago by • 0
0
votes
0
replies
132
views
Empty table plot using plotGseaTable()
FGSEA
3 days ago by Chris ▴ 260
0
votes
1
reply
180
views
VG : No reference-sense paths available in the graph; falling back to generic paths.
vg
updated 4 days ago by ▴ 120 • written 4 days ago by • 0
1
vote
3
replies
234
views
DiffBind: no peaks in DBA
MACS2 DiffBind ChIP-seq
updated 4 days ago by ★ 16k • written 4 days ago by ▴ 10
3
votes
5
replies
314
views
Converting CRAM to FastQ
GATK samtools cram SamToFastq fastq
3 days ago by Maverick ▴ 10
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk genomicsdbimport
updated 4 days ago by • 0 • written 5.1 years ago by 11k
0
votes
2
replies
191
views
Base Quality Score Recalibration with different reference genome
SNPs GATK BQSR RNA-seq
4 days ago by dtnondorf • 0
0
votes
5
replies
348
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core 16S amplicon dada2 ampliseq
updated 6 hours ago by ▴ 390 • written 4 days ago by ▴ 90
1
vote
2
replies
236
views
RNA-seq data for deep learning classification
rna-seq
3 days ago by yahn • 0
2
votes
8
replies
469
views
How to access TCGA samples that were treated with a specific drug?
TCGA RNA-seq
8 hours ago by Qroid ▴ 40
0
votes
1
reply
511
views
Loss of 'var' using concatenation of AnnData objects
Scanpy AnnData
updated 4 days ago by • 0 • written 4 months ago by • 0
0
votes
1
reply
150
views
Provean help
variant Provean
updated 4 days ago by ★ 27k • written 4 days ago by • 0
1
vote
1
reply
163
views
Download eQTL data of one specific gene for all tissues from GTEx
eQTL GTEx
updated 4 days ago by ★ 2.4k • written 4 days ago by ▴ 20
1
vote
1
reply
170
views
Super ehancers
enhancers
updated 4 days ago by ★ 16k • written 4 days ago by • 0
0
votes
6
replies
293
views
How does gene length effect the number of reads mapped
RNA-seq CPM sequencing
updated 3 days ago by ★ 6.0k • written 4 days ago by • 0
5
votes
5
replies
280
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA DADA2 metabarcoding
updated 4 days ago by ▴ 30 • written 4 days ago by ▴ 150
1
vote
7
replies
443
views
Downsampling long-read BAM files
nanopore BAM QC ONT downsampling
3 days ago by eebloom ▴ 80
3
votes
3
replies
327
views
What analysis suitable to identify similarly expressed genes between two samples (treated vs untreated). Contrary to DGE analysis,
Gene-Expression RNA NOISeq DGE
updated 3 days ago by 82k • written 4 days ago by • 0
0
votes
0
replies
100
views
Use of annotation of integrated Seurat object in single sample
Seurat
4 days ago by Bine ▴ 60
0
votes
0
replies
106
views
News: Beyond beginner R: Advancing your coding skills - September 16-19
Advanced-Coding Programming R
updated 4 days ago by 43k • written 4 days ago by ★ 2.5k
0
votes
1
reply
227
views
Subsetting and merging back Seurat Object brings different results
Seurat
4 days ago by Bine ▴ 60
0
votes
0
replies
142
views
Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
NGS Genomics Post-doc R-loops
updated 4 days ago by 43k • written 4 days ago by • 0
1
vote
1
reply
138
views
Discrepancy in read counts from fastq
downsampling fastq
updated 4 days ago by 43k • written 4 days ago by ▴ 90
0
votes
0
replies
96
views
Successfully identified and Masked rpeats using RM. What Next?
sequence annotation repeatmasker illumina assembly
4 days ago by Vijith ▴ 30
975 results • Page 2 of 20
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Answer: MSA and distance matrix in R
Comment: MSA and distance matrix in R
Comment: Which hg38 file?
Answer: Which hg38 file?
Answer: Where to get the following bed file?
How to save GRanges object to csv file
Answer: How to get proteins from GFF file resulted from MAKER annotation
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Recent Replies
Comment: HCL database download by sooni ▴ 20
I would like to download top markers for each subpopulation data. Is there no way? It seems different from the DGE data.
Comment: Understanding STAR output (Aligned.out.sam file) by GenoMax 142k
Refer to SAM alignment format: https://samtools.github.io/hts-specs/SAMv1.pdf Check section 1.4.
Answer: Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genom by LChart 3.9k
Step 1: Go to TCGA in the GDC and open the Cohort Builder https://portal.gdc.cancer.gov/analysis_page?app=CohortBuilder&tab=general Step …
Comment: Where to get the following bed file? by GenoMax 142k
SeqCap kits are discontinued. If you don't find the said file your will need to email Roche Support per this page: https://sequencing.roche…
Answer: Where to get the following bed file? by LChart 3.9k
UCSC maintains a list of exome probe sets and targets. You could check there: https://hgdownload.soe.ucsc.edu/gbdb/hg19/exomeProbesets/
Comment: How to compute TPM normalized values for TCGA miRNA data? by Ngrin • 0
Yes, I found some similar ideas on biostar repository. So you think the authors have done something wrong? And I should only consider CPM?
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA by Chris Dean ▴ 390
It is difficult to answer how they were able to identify *S. hominis* without seeing the code or paper. To address your second question, i…
Comment: Problem with Seurat package in PercentageFeatureSet function by bk11 ★ 2.4k
Did you check where the `features.tsv.gz` file had Gene IDs or Ensembl IDs?
Answer: How to compute TPM normalized values for TCGA miRNA data? by dsull ★ 6.0k
TPM is irrelevant for miRNA-seq; CPM works fine. TPM tries to adjust for length effects by dividing by gene length (e.g. reducing the im…
Comment: Applying the metacell2 algorithm using python by Wayne ★ 2.0k
"I'm also unsure what qualifies as a lateral gene." The [README where you reference](https://metacells.readthedocs.io/en/latest/readme.htm…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA by sovrappensiero ▴ 90
Ah, yes this makes sense! I knew this was an issue with, say, using kraken2 on shotgun metagenomic reads, but I don't have a lot of experi…
Comment: How to access TCGA samples that were treated with a specific drug? by Qroid ▴ 40
Thank you. Maybe it's best to confirm with the authors about how they're getting responder/non-responder labels. I'll do that now.
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA by Chris Dean ▴ 390
If you sequenced a short hypervariable region, most of your sequence reads will not be able to be assigned to the species level. One possi…
Comment: anRichment is missing by GenoMax 142k
Consider emailing Dr. Horvath about this. Until enough people make him aware of this issue WGCNA "problem" is unlikely to get fixed.
Comment: anRichment is missing by Tatyana • 0
Unfortunately, there are only tutorials and codes for tutorials for WGCNA, not installation files for any their packages... :(
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