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29
votes
28
replies
34k
views
11 follow
Split Fastq Files Into Chunks Of 1M Reads
split fastq
updated 3 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 8 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
2.3k
views
Extract gRNA sequence using cutadapt
cutadapt trimming crispr sequencing
updated 3 days ago by 142k • written 4.5 years ago by ▴ 20
16
votes
12
replies
7.3k
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 6 hours ago by • 0 • written 6.1 years ago by ▴ 20
9
votes
10
replies
501
views
6 follow
Bacterial plasmid analysis
bacteria plasmid wgs hybridassembly sequencing
updated 3 days ago by ▴ 20 • written 4 days ago by • 0
0
votes
10
replies
526
views
Low mapping rate with Salmon
RNA-seq Salmon Quantification
updated 6 days ago by 19k • written 13 days ago by • 0
1
vote
10
replies
815
views
error to run rnammer
phylogenomics rRNA_extraction rnammer
updated 3 hours ago by • 0 • written 3 months ago by ▴ 30
40
votes
10
replies
42k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma sva Combat batch-effect
updated 6 days ago by ▴ 40 • written 6.7 years ago by ★ 1.3k
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference 38build impute imputation
6 days ago by anna ▴ 20
9
votes
9
replies
556
views
High Malat-1 expression in single cell data
single-cell
updated 1 day ago by 43k • written 6 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 2 days ago by • 0 • written 2.2 years ago by • 0
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk genomicsdbimport
updated 3 days ago by • 0 • written 5.1 years ago by 11k
0
votes
8
replies
441
views
What does it mean single base resolution in sequencing?
SNP sequencing
updated 5 days ago by 4.2k • written 7 days ago by ▴ 10
1
vote
8
replies
477
views
Downsampling fastq file
downsample fastq
5 days ago by marco.barr ▴ 90
1
vote
7
replies
436
views
Downsampling long-read BAM files
nanopore BAM QC ONT downsampling
2 days ago by eebloom ▴ 80
1
vote
7
replies
528
views
ScRNA data question
scRNA Vlnplot Samples
updated 6 days ago by ★ 2.4k • written 10 days ago by ▴ 10
3
votes
7
replies
347
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc cutadapt illumina tile paired-end
6 days ago by salias • 0
2
votes
7
replies
421
views
How to access TCGA samples that were treated with a specific drug?
TCGA RNA-seq
updated 1 day ago by ★ 1.2k • written 3 days ago by ▴ 40
4
votes
7
replies
591
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity scVelo scRNA-seq splicing
6 days ago by e.r.zakiev ▴ 210
0
votes
7
replies
541
views
Post-imputation plot
michigan-imputation-server quality-control
updated 3 days ago by 3.9k • written 6 days ago by ▴ 10
5
votes
6
replies
1.8k
views
agilent human all exon sureselct v7 bed file
exon human bed v7 agilent all sureselect
updated 17 hours ago by ▴ 10 • written 24 months ago by • 0
1
vote
6
replies
2.8k
views
Segmentation fault using gemma
gemma gwas
updated 6 days ago by • 0 • written 4.9 years ago by ▴ 90
0
votes
6
replies
374
views
Differential Expression Analysis using DESeq2 in R
deseq2 R
updated 2 days ago by 14k • written 2 days ago by • 0
4
votes
6
replies
3.9k
views
Taking the difference of two VCFs (or removing singletons)
genome sequencing singleton SNP filter
updated 5 days ago by ▴ 20 • written 9.6 years ago by ▴ 40
1
vote
6
replies
339
views
Do I need to go back and filter my long-reads?
alignment nanopore filtering QC ONT
updated 2 days ago by 142k • written 20 days ago by ▴ 80
5
votes
6
replies
523
views
Programmatically retrieving positions of protein active site residues
Uniprot PDB Proteins
updated 5 days ago by ▴ 760 • written 6 days ago by ▴ 40
0
votes
6
replies
286
views
How does gene length effect the number of reads mapped
RNA-seq CPM sequencing
updated 2 days ago by ★ 6.0k • written 3 days ago by • 0
3
votes
5
replies
263
views
Generating mpileup file using samtools
mpileup samtools
updated 2 days ago by 21k • written 3 days ago by • 0
0
votes
5
replies
423
views
How should I make kallisto indexes?
kallisto
updated 6 days ago by ★ 6.0k • written 20 days ago by ▴ 150
1
vote
5
replies
328
views
Introduce SNPs on FASTA
simulation snps haplotypes pharmacogenetics
3 days ago by Riccardo ▴ 10
5
votes
5
replies
268
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA DADA2 metabarcoding
updated 3 days ago by ▴ 30 • written 3 days ago by ▴ 150
2
votes
5
replies
930
views
Retrieval of Active site information programmatically
Catalytic Python Active PDB site Site
updated 6 days ago by ★ 2.0k • written 2.0 years ago by • 0
0
votes
5
replies
307
views
Easy way to find out which allele is minor allele from bed file?
plink
updated 2 days ago by 10k • written 2 days ago by ▴ 750
0
votes
5
replies
339
views
6 follow
What purposes can TPM values be used for?
RNA-seq TPM Normalization DESeq2
updated 3 days ago by ▴ 180 • written 3 days ago by • 0
0
votes
5
replies
310
views
RNAseq one control two conditions, shared and exclusive genes
conditions RNAseq multiple Rstudio
updated 3 days ago by ▴ 20 • written 6 days ago by • 0
3
votes
5
replies
305
views
Converting CRAM to FastQ
GATK samtools cram SamToFastq fastq
2 days ago by Maverick ▴ 10
5
votes
5
replies
577
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 2 days ago by • 0 • written 11 days ago by ★ 3.9k
0
votes
5
replies
371
views
Telescope issue
Telescope RNA-seq
updated 4 days ago by 142k • written 5 days ago by • 0
1
vote
4
replies
224
views
install package: package ‘gmwm’ is not available for this version of R
install.packages r
updated 1 hour ago by 11k • written 19 hours ago by • 0
1
vote
4
replies
1.1k
views
Filtering qscore on dorado
dorado filtering QC nanopore Guppy
3 days ago by eebloom ▴ 80
2
votes
4
replies
2.6k
views
When to use .vcf or .gvcf files from GATK HaplotypeCaller?
indel gatk calling snp variant
updated 6 days ago by 9.7k • written 24 months ago by ▴ 120
1
vote
4
replies
396
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray Limma Agilent
6 days ago by hagl ▴ 10
0
votes
4
replies
263
views
Genbank File Format
gbkformat
6 days ago by alenew.am • 0
1
vote
4
replies
295
views
Segmentation error while using a tool
smalt
updated 1 day ago by ★ 27k • written 2 days ago by • 0
0
votes
4
replies
273
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
2
votes
4
replies
293
views
from row count to tpm
tpm row-count normalization
updated 5 days ago by 43k • written 13 days ago by ▴ 20
5
votes
4
replies
376
views
Forum: Ideal PC configurations and operating system for bioinformatics laboratory
PC
3 days ago by Estevão • 0
0
votes
4
replies
93
views
install.packages("imudata") - package ‘imudata’ is not available for this version of R
install.packages r
1 hour ago by snajafy • 0
186 results • Page 1 of 4
Recent Votes
Answer: Hide positions in alignment with 99% "–" characters to ignore single sequence in
Answer: Hide positions in alignment with 99% "–" characters to ignore single sequence in
Answer: Association study using SNP data
.lgen file has 3+ different alleles
Force PLINK2 to neglect chrX as the sex chromosome
Answer: Force PLINK2 to neglect chrX as the sex chromosome
LD-prune variants while maintaining a list of SNPs
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Answer: Tissue-specific DEG analysis with DEseq2 by ATpoint 82k
I assume that all data are from the same experiment, without batch effects and can thus be quantitiatively compared: Many ways to do thi…
Comment: install.packages("imudata") - package ‘imudata’ is not available for this versio by snajafy • 0
I am facing the same problem and I don't know how to solve the problem,....
Comment: install.packages("imudata") by zx8754 11k
[How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning?](https://stackoverflow.com/q/25721884/680068)
Answer: install.packages("imudata") by ATpoint 82k
Welcome to this community. Please learn the most important lesson right away which is reading answers and learning from it. Users gave you …
Comment: install.packages("imudata") by marco.barr ▴ 90
You can install from github directly. Many R packages are not present in the CRAN repository or in Bioconductor( from Biocmanager). Also re…
Comment: install package by snajafy • 0
Hi, Thanks for your answer, I do it, but I get this error: ERROR: compilation failed for package 'gmwm' removing 'C:/Users/najafi/AppData/…
Comment: Quetion regarding WGCNA by andres.firrincieli 3.6k
There is something wrong with your data but without any context I can't really answer to your question. I would like to see a PCA plot of …
Comment: error to run rnammer by antonio.spl • 0
please could you tell me what was the solution, I am having the same problem, I only get empty files.
Comment: install package by snajafy • 0
Hi, Thanks for your answer, I do it, but I get this error: ERROR: compilation failed for package 'gmwm' * removing 'C:/Users/najafi/AppData…
Answer: Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so t by swbarnes2 14k
Any chance the numerical columns were imported as factors?
Comment: ERROR When Using Ensembl Plants Biomart Wget API by Dora ▴ 10
Thank you very much, that works perfectly :) ! Maybe someone needs to use a plant dataset as an example (instead of human dataset ) in the …
Comment: Truncated Bam Error by guanghao • 0
I also have this problem, but it doesn't work even I remove the Xms32g. The result bam is still malformed.
Answer: DMRcate ranges liftover hg19 to hg38 by aaron.stevens • 0
Hey, I believe they are mapped to hg19 and this is potentially a bigger problem than people realise, I nearly made this mistake and I would…
Comment: STRING-DB API can't find my protein but I can find it when I go to the STRING-DB by brandon • 0
This worked beautifully using 'requests.get()' in python, thank you so much!
Answer: STRING-DB API can't find my protein but I can find it when I go to the STRING-DB by Pierre Lindenbaum 161k
first get the main ID in stringdb: $ wget -qO - "https://string-db.org/api/tsv-no-header/get_string_ids?identifiers=RPS4Y1&species=960…
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