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29
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28
replies
34k
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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
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
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
1
vote
14
replies
2.4k
views
Extract gRNA sequence using cutadapt
cutadapt trimming crispr sequencing
updated 4 days ago by 142k • written 4.5 years ago by ▴ 20
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
1
vote
11
replies
5.5k
views
Truncated Bam Error
R next-gen sequencing software error
updated 17 hours ago by • 0 • written 6.1 years ago by ▴ 20
0
votes
10
replies
530
views
Low mapping rate with Salmon
RNA-seq Salmon Quantification
updated 6 days ago by 19k • written 14 days ago by • 0
1
vote
10
replies
838
views
error to run rnammer
phylogenomics rRNA_extraction rnammer
updated 14 hours ago by • 0 • written 3 months 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
10
votes
10
replies
613
views
High Malat-1 expression in single cell data
single-cell
updated 9 hours ago by ▴ 10 • written 7 days ago by ▴ 30
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
0
votes
8
replies
442
views
What does it mean single base resolution in sequencing?
SNP sequencing
updated 6 days ago by 4.2k • written 8 days ago by ▴ 10
1
vote
8
replies
480
views
Downsampling fastq file
downsample fastq
6 days ago by marco.barr ▴ 90
2
votes
8
replies
444
views
How to access TCGA samples that were treated with a specific drug?
TCGA RNA-seq
2 hours ago by Qroid ▴ 40
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
1
vote
7
replies
441
views
Downsampling long-read BAM files
nanopore BAM QC ONT downsampling
3 days ago by eebloom ▴ 80
0
votes
7
replies
550
views
Post-imputation plot
michigan-imputation-server quality-control
updated 3 days ago by 3.9k • written 7 days 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
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
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
0
votes
6
replies
397
views
Differential Expression Analysis using DESeq2 in R
deseq2 R
updated 3 days ago by 14k • written 3 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
1
vote
6
replies
548
views
anRichment is missing
WGCNA anRichment
updated 3 hours ago by 142k • written 5 months ago by ▴ 180
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq RNA-Seq exon
updated 7 hours ago by ▴ 30 • written 6.7 years ago by ★ 1.2k
1
vote
6
replies
341
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
0
votes
5
replies
280
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 26 minutes ago by ▴ 390 • written 4 days ago by ▴ 90
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
0
votes
5
replies
375
views
Telescope issue
Telescope RNA-seq
updated 5 days ago by 142k • written 6 days ago by • 0
1
vote
5
replies
330
views
Introduce SNPs on FASTA
simulation snps haplotypes pharmacogenetics
3 days ago by Riccardo ▴ 10
0
votes
5
replies
312
views
RNAseq one control two conditions, shared and exclusive genes
conditions RNAseq multiple Rstudio
updated 3 days ago by ▴ 20 • written 7 days ago by • 0
1
vote
5
replies
243
views
install.packages("imudata") - package ‘imudata’ is not available for this version of R
r
updated 8 hours ago by 43k • written 14 hours ago by • 0
0
votes
5
replies
324
views
Easy way to find out which allele is minor allele from bed file?
plink
updated 2 days ago by 10k • written 3 days ago by ▴ 750
1
vote
5
replies
310
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 7 hours ago by 43k • written 1 day ago by • 0
5
votes
5
replies
278
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
3
votes
5
replies
310
views
Converting CRAM to FastQ
GATK samtools cram SamToFastq fastq
3 days ago by Maverick ▴ 10
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
0
votes
5
replies
343
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
4
replies
314
views
Segmentation error while using a tool
smalt
updated 2 days ago by ★ 27k • written 2 days ago by • 0
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
3
votes
4
replies
363
views
Design matrix Differential expression analysis
RNA-seq Differential-expression
7 hours ago by SHN ▴ 40
0
votes
4
replies
275
views
Perfom a Gene Ontology Analysis from GO terms txt file
RNA-Seq GO
updated 6 days ago by 43k • written 6 days ago by ▴ 50
0
votes
4
replies
281
views
Question regarding WGCNA
WGCNA Network-construction
updated 4 hours ago by 3.6k • written 2 days ago by • 0
1
vote
4
replies
1.1k
views
Filtering qscore on dorado
dorado filtering QC nanopore Guppy
4 days ago by eebloom ▴ 80
5
votes
4
replies
377
views
Forum: Ideal PC configurations and operating system for bioinformatics laboratory
PC
4 days ago by Estevão • 0
0
votes
4
replies
263
views
Genbank File Format
gbkformat
6 days ago by alenew.am • 0
1
vote
3
replies
281
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
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
0
votes
3
replies
286
views
KEGG Pathways
r RNA-seq
updated 6 days ago by 43k • written 6 days ago by • 0
2
votes
3
replies
273
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
3
replies
788
views
Issues with Mixture file when using CIBERSORTx
Deconvolution CIBERSORTx
updated 2 days ago by • 0 • written 7 months ago by • 0
176 results • Page 1 of 4
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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
Comment: Gene Specific coverage from WGS data
Comment: Gene Specific coverage from WGS data
Comment: High Malat-1 expression in single cell data
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Recent Replies
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…
Comment: Question regarding WGCNA by andres.firrincieli 3.6k
the within-group variability is so small that these look like technical replicates rather than independent biological replicates
Answer: Gene ontology and homologs by geneontologyhelp ▴ 400
No. Homology is defined as shared common ancestry. Two genes that take part in the same biological process may not have the same functio…
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