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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
615
views
High Malat-1 expression in single cell data
single-cell
updated 14 hours ago by ▴ 10 • written 7 days ago by ▴ 30
9
votes
10
replies
512
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
5
replies
586
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
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
6
replies
525
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
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
380
views
Forum: Ideal PC configurations and operating system for bioinformatics laboratory
PC
4 days ago by Estevão • 0
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq RNA-Seq exon
updated 12 hours ago by ▴ 30 • written 6.7 years ago by ★ 1.2k
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
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
1
reply
200
views
LD-prune variants while maintaining a list of SNPs
snp vcf plink filtering independent
updated 18 hours ago by 11k • written 2 days ago by ▴ 560
4
votes
2
replies
229
views
GRCh38.gmap file
gnomix gmap
2 days ago by lorena9132 ▴ 10
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
5
replies
314
views
Converting CRAM to FastQ
GATK samtools cram SamToFastq fastq
3 days ago by Maverick ▴ 10
3
votes
5
replies
271
views
Generating mpileup file using samtools
mpileup samtools
updated 3 days ago by 21k • written 3 days ago by • 0
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
3
votes
4
replies
377
views
Design matrix Differential expression analysis
RNA-seq Differential-expression
updated 4 hours ago by ★ 7.1k • written 3 days ago by ▴ 40
3
votes
2
replies
385
views
Extract protein sequence
fasta alignment blast
6 days ago by anna ▴ 20
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
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
1
reply
289
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
updated 3 days ago by 10k • written 6 days ago by ▴ 10
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
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
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
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
2
votes
2
replies
184
views
Gene Specific coverage from WGS data
linux WGS Bioinformatics SARS CoV2
updated 14 hours ago by 142k • written 6 days ago by • 0
2
votes
8
replies
469
views
How to access TCGA samples that were treated with a specific drug?
TCGA RNA-seq
7 hours ago by Qroid ▴ 40
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
286
views
Association study using SNP data
Association Allele Parentage SNP
1 day ago by drajangirija • 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
2
votes
2
replies
275
views
p-value in CIBERSORT
CIBERSORT p-value
5 days ago by michelafrancesconi9 ▴ 20
2
votes
3
replies
798
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
195
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
1 day ago by brandon • 0
1
vote
1
reply
234
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
175
views
Including plasmid in alignment
Bacteria Transcriptomics BOWTIE2 STAR
6 days ago by heelpPlease • 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
6
replies
344
views
Do I need to go back and filter my long-reads?
alignment nanopore filtering QC ONT
updated 3 days ago by 142k • written 21 days ago by ▴ 80
1
vote
0
replies
189
views
News: Landscape Genomics course in Switzerland
LFMM Landscape-Genomics Sambada R Local-Adaptation
4 days ago by carlopecoraro2 ★ 2.5k
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
482
views
Downsampling fastq file
downsample fastq
6 days ago by marco.barr ▴ 90
1
vote
1
reply
235
views
Polishing genome assembly
polishing Nanopore PacBio
updated 6 days ago by 54k • written 7 days ago by • 0
1
vote
3
replies
239
views
Odd alignment question/finding
Alignment
updated 3 days ago by ★ 2.1k • written 5 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
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
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
176 results • Page 1 of 4
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Answer: How to get proteins from GFF file resulted from MAKER annotation
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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... :(
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…
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