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175 results • Page 1 of 4
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38
votes
24
replies
2.0k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq STAR NGS Illumina
updated 6 days ago by 19k • written 9 days ago by ▴ 580
29
votes
28
replies
34k
views
11 follow
Split Fastq Files Into Chunks Of 1M Reads
split fastq
updated 4 days ago by • 0 • written 12.8 years ago by ★ 1.7k
16
votes
12
replies
7.4k
views
10 follow
how to split multi-fasta file into single fasta file named by header
genome perl python3 bash python
updated 3 days ago by ▴ 10 • written 3.1 years ago by ▴ 120
10
votes
10
replies
614
views
High Malat-1 expression in single cell data
single-cell
updated 10 hours ago by ▴ 10 • written 7 days ago by ▴ 30
9
votes
10
replies
511
views
6 follow
Bacterial plasmid analysis
bacteria plasmid wgs hybridassembly sequencing
updated 4 days ago by ▴ 20 • written 5 days ago by • 0
5
votes
3
replies
282
views
6 follow
Integrate transcriptomic data and proteomics data.
OMICS
updated 6 days ago by ★ 1.2k • written 6 days ago by • 0
5
votes
4
replies
377
views
Forum: Ideal PC configurations and operating system for bioinformatics laboratory
PC
4 days ago by Estevão • 0
5
votes
6
replies
1.8k
views
agilent human all exon sureselct v7 bed file
exon human bed v7 agilent all sureselect
updated 1 day ago by ▴ 10 • written 24 months ago by • 0
5
votes
5
replies
585
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 3 days ago by • 0 • written 11 days ago by ★ 3.9k
5
votes
6
replies
524
views
Programmatically retrieving positions of protein active site residues
Uniprot PDB Proteins
updated 6 days ago by ▴ 760 • written 7 days ago by ▴ 40
5
votes
5
replies
279
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
4
votes
6
replies
3.9k
views
Taking the difference of two VCFs (or removing singletons)
genome sequencing singleton SNP filter
updated 6 days ago by ▴ 20 • written 9.6 years ago by ▴ 40
4
votes
15
replies
1.6k
views
how to test for differential expression in samples where a global increase in gene expression is expected
edgeR DESeq Differential-Expression RNA-Seq
updated 2 days ago by ★ 7.1k • written 4 months ago by ▴ 10
4
votes
1
reply
195
views
LD-prune variants while maintaining a list of SNPs
snp vcf plink filtering independent
updated 13 hours ago by 11k • written 2 days ago by ▴ 560
4
votes
2
replies
223
views
GRCh38.gmap file
gnomix gmap
1 day ago by lorena9132 ▴ 10
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq RNA-Seq exon
updated 8 hours ago by ▴ 30 • written 6.7 years ago by ★ 1.2k
4
votes
9
replies
2.1k
views
6 follow
Same sequencing sample in multiple lanes. How to analyse it?
sequencing bowtie2 alignment samtools ngs
updated 3 days ago by • 0 • written 2.2 years ago by • 0
3
votes
2
replies
385
views
Extract protein sequence
fasta alignment blast
6 days ago by anna ▴ 20
3
votes
5
replies
310
views
Converting CRAM to FastQ
GATK samtools cram SamToFastq fastq
3 days ago by Maverick ▴ 10
3
votes
5
replies
270
views
Generating mpileup file using samtools
mpileup samtools
updated 3 days ago by 21k • written 3 days ago by • 0
3
votes
3
replies
323
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
3
votes
4
replies
369
views
Design matrix Differential expression analysis
RNA-seq Differential-expression
updated just now by ★ 7.1k • written 3 days ago by ▴ 40
3
votes
0
replies
1.1k
views
Tool: Sars-Cov-2 Genome & ACE 2 Exploration
sequence alignment SNP genome
1 day ago by Ibrahim Tanyalcin ★ 1.2k
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
2
votes
2
replies
182
views
Gene Specific coverage from WGS data
linux WGS Bioinformatics SARS CoV2
updated 9 hours ago by 142k • written 6 days ago by • 0
2
votes
1
reply
278
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
updated 2 days ago by 10k • written 6 days ago by ▴ 10
2
votes
2
replies
1.8k
views
Parametric or non-parametric tests for qPCR significance testing between treatments?
qPCR statistical test parametric non-parametric
updated 3 days ago by ▴ 210 • written 3.8 years ago by ▴ 40
2
votes
2
replies
208
views
Raw counts using stringtie
stringtie RNA-seq
updated 3 days ago by 142k • written 3 days ago by • 0
2
votes
2
replies
2.6k
views
Pindel Segmentation Fault Error
pindel
updated 2 days ago by • 0 • written 10.2 years ago by ▴ 20
2
votes
4
replies
296
views
from row count to tpm
tpm row-count normalization
updated 6 days ago by 43k • written 14 days ago by ▴ 20
2
votes
2
replies
201
views
MA plot of shrunken fold change
MA-plot Deseq2
updated 6 days ago by 82k • written 6 days ago by • 0
2
votes
3
replies
274
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
2
votes
8
replies
454
views
How to access TCGA samples that were treated with a specific drug?
TCGA RNA-seq
3 hours ago by Qroid ▴ 40
2
votes
2
replies
185
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
23 hours ago by brandon • 0
2
votes
2
replies
279
views
Association study using SNP data
Association Allele Parentage SNP
1 day ago by drajangirija • 0
2
votes
2
replies
274
views
p-value in CIBERSORT
CIBERSORT p-value
5 days ago by michelafrancesconi9 ▴ 20
2
votes
3
replies
789
views
Issues with Mixture file when using CIBERSORTx
Deconvolution CIBERSORTx
updated 2 days ago by • 0 • written 7 months ago by • 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
1
vote
1
reply
233
views
Adjust pvalue in R with different approach give me all different outcome
statistics R p-value
updated 6 days ago by 43k • written 6 days ago by ▴ 60
1
vote
1
reply
173
views
Including plasmid in alignment
Bacteria Transcriptomics BOWTIE2 STAR
6 days ago by heelpPlease • 0
1
vote
1
reply
235
views
Polishing genome assembly
polishing Nanopore PacBio
updated 6 days ago by 54k • written 6 days ago by • 0
1
vote
3
replies
282
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA illumina GEO metadata
updated 6 days ago by 142k • written 6 days ago by • 0
1
vote
2
replies
252
views
POSSUM not working due to incompatible pssm file
fasta pse-pssm pssm POSSUM
4 days ago by rianna.collins • 0
1
vote
8
replies
480
views
Downsampling fastq file
downsample fastq
6 days ago by marco.barr ▴ 90
1
vote
2
replies
235
views
RNA-seq data for deep learning classification
rna-seq
3 days ago by yahn • 0
1
vote
2
replies
228
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana gtf reference-genome
updated 6 days ago by 43k • written 6 days ago by • 0
1
vote
7
replies
441
views
Downsampling long-read BAM files
nanopore BAM QC ONT downsampling
3 days ago by eebloom ▴ 80
1
vote
2
replies
280
views
read length in structural variant calling
nanopore SV QC ONT variant
3 days ago by eebloom ▴ 80
1
vote
3
replies
309
views
DESeq2 processing problems
deseq2 R
updated 5 days ago by 82k • written 5 days ago by • 0
1
vote
5
replies
330
views
Introduce SNPs on FASTA
simulation snps haplotypes pharmacogenetics
3 days ago by Riccardo ▴ 10
175 results • Page 1 of 4
Recent Votes
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
Answer: Gene ontology and homologs
Comment: anRichment is missing
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Recent Replies
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... :(
Comment: anRichment is missing by GenoMax 142k
See this link for the WGCNA documentation and code from Peter Langfelder : https://bioinformatics.stackexchange.com/questions/21885/where-t…
Comment: anRichment is missing by Tatyana • 0
The problem is back, Horwath's lab web is down again. Is it possible to get anRichment istallation file somewhere? (The greater problem is …
Comment: 16S rRNA microbiome differential abundance analysis with DESeq2 finds same micro by andres.firrincieli 3.6k
1. Maribaculaceae is a family not a genus 2. Who said that ASV with the same taxonomic classification must have the same behaviour? 3. With…
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