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171 results • Page 1 of 4
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29
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28
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34k
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11 follow
Split Fastq Files Into Chunks Of 1M Reads
split fastq
updated 5 days ago by • 0 • written 12.8 years ago by ★ 1.7k
10
votes
16
replies
17k
views
7 follow
How Can I Count Snps In My Final Vcf Files
SNP
updated 15 hours ago by 161k • written 5.7 years ago by ▴ 180
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 3 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 5 days ago by 142k • written 4.5 years ago by ▴ 20
10
votes
14
replies
633
views
6 follow
Bacterial plasmid analysis
bacteria plasmid wgs hybridassembly sequencing
updated 11 hours ago by 142k • written 6 days ago by • 0
12
votes
13
replies
717
views
High Malat-1 expression in single cell data
single-cell
updated 9 hours ago by ★ 6.0k • written 8 days ago by ▴ 30
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 4 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 1 day ago by • 0 • written 6.1 years ago by ▴ 20
1
vote
10
replies
841
views
error to run rnammer
phylogenomics rRNA_extraction rnammer
updated 1 day ago by • 0 • written 3 months 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 4 days ago by • 0 • written 2.2 years ago by • 0
3
votes
8
replies
499
views
How to access TCGA samples that were treated with a specific drug?
TCGA RNA-seq
1 day ago by Qroid ▴ 40
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk genomicsdbimport
updated 5 days ago by • 0 • written 5.1 years ago by 11k
1
vote
7
replies
448
views
Downsampling long-read BAM files
nanopore BAM QC ONT downsampling
4 days ago by eebloom ▴ 80
0
votes
7
replies
556
views
Post-imputation plot
michigan-imputation-server quality-control
updated 4 days ago by 3.9k • written 8 days ago by ▴ 10
1
vote
7
replies
468
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 2 hours ago by ▴ 400 • written 5 days ago by ▴ 90
0
votes
6
replies
412
views
Differential Expression Analysis using DESeq2 in R
deseq2 R
updated 4 days ago by 14k • written 4 days ago by • 0
5
votes
6
replies
1.8k
views
agilent human all exon sureselct v7 bed file
exon human bed v7 agilent all sureselect
updated 2 days ago by ▴ 10 • written 24 months ago by • 0
1
vote
6
replies
352
views
Do I need to go back and filter my long-reads?
alignment nanopore filtering QC ONT
updated 4 days ago by 142k • written 22 days ago by ▴ 80
0
votes
6
replies
303
views
How does gene length effect the number of reads mapped
RNA-seq CPM sequencing
updated 4 days ago by ★ 6.0k • written 5 days ago by • 0
1
vote
6
replies
653
views
anRichment is missing
WGCNA anRichment
updated 1 day ago by 142k • written 5 months ago by ▴ 180
1
vote
6
replies
403
views
Question regarding WGCNA
WGCNA Network-construction
updated 8 hours ago by 3.6k • written 4 days ago by • 0
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq RNA-Seq exon
updated 1 day ago by ▴ 30 • written 6.7 years ago by ★ 1.2k
3
votes
5
replies
321
views
Converting CRAM to FastQ
GATK samtools cram SamToFastq fastq
4 days ago by Maverick ▴ 10
5
votes
5
replies
195
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
20 minutes ago by Chris ▴ 280
1
vote
5
replies
332
views
Introduce SNPs on FASTA
simulation snps haplotypes pharmacogenetics
4 days ago by Riccardo ▴ 10
0
votes
5
replies
378
views
Telescope issue
Telescope RNA-seq
updated 6 days ago by 142k • written 7 days ago by • 0
0
votes
5
replies
356
views
6 follow
What purposes can TPM values be used for?
RNA-seq TPM Normalization DESeq2
updated 4 days ago by ▴ 180 • written 5 days ago by • 0
0
votes
5
replies
340
views
Easy way to find out which allele is minor allele from bed file?
plink
updated 3 days ago by 10k • written 4 days ago by ▴ 750
5
votes
5
replies
280
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA DADA2 metabarcoding
updated 5 days ago by ▴ 30 • written 5 days ago by ▴ 150
3
votes
5
replies
277
views
Generating mpileup file using samtools
mpileup samtools
updated 4 days ago by 21k • written 4 days ago by • 0
0
votes
5
replies
266
views
Applying the metacell2 algorithm using python
python single-cell scanpy metacell2
updated 4 hours ago by 43k • written 1 day ago by ▴ 140
0
votes
5
replies
319
views
RNAseq one control two conditions, shared and exclusive genes
conditions RNAseq multiple Rstudio
updated 4 days ago by ▴ 20 • written 8 days ago by • 0
1
vote
5
replies
155
views
UMI-Tools knee-method has great influence on the results of white list
single-cell whitelist UMI RNA UMI-Tools
updated 9 hours ago by 19k • written 12 hours ago by ★ 1.8k
1
vote
5
replies
280
views
install.packages("imudata") - package ‘imudata’ is not available for this version of R
r
updated 1 day ago by 43k • written 1 day ago by • 0
1
vote
5
replies
351
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 1 day ago by 43k • written 2 days ago by • 0
5
votes
5
replies
601
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 4 days ago by • 0 • written 12 days ago by ★ 3.9k
2
votes
4
replies
709
views
Count all variants from vcf file
variants vcf Count
updated 15 hours ago by 161k • written 20 months ago by • 0
0
votes
4
replies
369
views
Highest variable features in single cell data
single-cell
13 hours ago by carolofharvest ▴ 30
0
votes
4
replies
289
views
HCL database download
database HCL human
updated 11 hours ago by 142k • written 3 days ago by ▴ 20
1
vote
4
replies
345
views
Segmentation error while using a tool
smalt
updated 3 days ago by ★ 27k • written 3 days ago by • 0
1
vote
4
replies
147
views
Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, Complexity, and Use Cases
fmindex bwt
1 hour ago by qwertyuiop26 • 0
5
votes
4
replies
385
views
Forum: Ideal PC configurations and operating system for bioinformatics laboratory
PC
5 days ago by Estevão • 0
1
vote
4
replies
1.1k
views
Filtering qscore on dorado
dorado filtering QC nanopore Guppy
5 days ago by eebloom ▴ 80
3
votes
4
replies
403
views
Design matrix Differential expression analysis
RNA-seq Differential-expression
updated 1 day ago by ★ 7.1k • written 4 days ago by ▴ 40
1
vote
4
replies
258
views
Understanding STAR output (Aligned.out.sam file)
STAR paired-end read
4 hours ago by heelpPlease • 0
0
votes
3
replies
187
views
How to compute TPM normalized values for TCGA miRNA data?
TCGA normalization TPM miRNA
updated 17 hours ago by 14k • written 1 day ago by • 0
1
vote
3
replies
274
views
TaxID mapping file
annotation blobtools RNAseq decontamination transcriptomes
2 days ago by Lada ▴ 30
3
votes
3
replies
334
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 4 days ago by 82k • written 5 days ago by • 0
1
vote
3
replies
241
views
Odd alignment question/finding
Alignment
updated 4 days ago by ★ 2.1k • written 5 days ago by • 0
2
votes
3
replies
813
views
Issues with Mixture file when using CIBERSORTx
Deconvolution CIBERSORTx
updated 3 days ago by • 0 • written 7 months ago by • 0
171 results • Page 1 of 4
Recent Votes
Answer: Tissue-specific DEG analysis with DEseq2
Answer: TFs and Gene databases
Answer: TFs and Gene databases
Comment: How to access TCGA samples that were treated with a specific drug?
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
Answer: TFs and Gene databases
Answer: TFs and Gene databases
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Recent Replies
Answer: barcode of TCR-sequencing by mizraelson ▴ 60
Hi, What protocol did you use for TCR-seq library preparation? Generally speaking, there is no need to remove barcodes, as MiXCR can work …
Comment: Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, C by qwertyuiop26 • 0
I've implemented fm index with backward search and need an inexact search to implement on FM index, I couldn't understand how fm index coul…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA by Chris Dean ▴ 400
The md5 hash they refer to on line 22 (f46a7ca244afef522b22a11bd33d27b1) appears to map to a *S. aureus* strain, not *S. hominis* (you can …
Comment: Correlating Bulk Differential Expression with quantitative by Qroid ▴ 40
You could try including disease scale for each sample as a design factor. See the vignette here https://bioconductor.org/packages/devel/bio…
Comment: Help with generating annotation database for dog genome to use in ANNOVAR for v by sainavyav22 • 0
Hello, Thanks for the reply. I could only see the refMrna.fa file in the link you provided. Where can I get the refGene.txt file. Thanks fo…
Answer: Understanding STAR output (Aligned.out.sam file) by heelpPlease • 0
After thoroughly reviewing all the documents again, I've identified the root cause of my initial issue: the failure to detect essential gen…
Comment: Understanding STAR output (Aligned.out.sam file) by heelpPlease • 0
Thank you! Now that I understand that there is a difference between read and fragment, I could actually find a lot of helpful information..…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA by sovrappensiero ▴ 90
Thanks again. Hmm...this makes me suspicious of whether this normalization is actually possible. In case you'd like to take a look, [here]…
Comment: Filtering Multi-sample VCF file for all except one Genotype by Jeremy Leipzig 22k
The seven genotypes being 58025AA, 58025AG, 58051TT, 58051TC, 58051CC, 58057TT, 58057TC
Answer: TFs and Gene databases by jared.andrews07 ★ 16k
See [TFlink](https://tflink.net/), [KnockTF2](https://bio.liclab.net/KnockTFv2/index.php), [TFBSDB](https://tfbsdb.systemsbiology.net/), an…
Comment: Filtering Multi-sample VCF file for all except one Genotype by GenoMax 142k
> Seven genotpyes have been sampled and all variants, which belong to one of those genotpyes are to be "erased" (or every other variant exc…
Comment: Filtering Multi-sample VCF file for all except one Genotype by Pierre Lindenbaum 161k
> , filter a multisample VCF file for all genotypes except one of them filter for what ?
Answer: Applying the metacell2 algorithm using python by Wayne ★ 2.0k
I had hoped things like [this Jupyter notebook for the rabbit data analysis](https://nbviewer.org/github/tanaylab/rabembflow/blob/master/2-…
Comment: Help with running egsea() by 1769mkc ★ 1.2k
please provide the design matrix mean the metadata of the model fit2 which is there in the code . i guess other users can help
Comment: Applying the metacell2 algorithm using python by JACKY ▴ 140
The repo does not provide any valuable information unfortunately. The Metacell algorithm they provide in the vignette is missing the metagr…
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