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179 results • Page 2 of 4
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1
vote
1
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172
views
Including plasmid in alignment
Bacteria Transcriptomics BOWTIE2 STAR
5 days ago by heelpPlease • 0
1
vote
1
reply
232
views
Adjust pvalue in R with different approach give me all different outcome
statistics R p-value
updated 5 days ago by 43k • written 5 days ago by ▴ 60
1
vote
2
replies
290
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast pssm
5 days ago by Nafi • 0
1
vote
3
replies
307
views
DESeq2 processing problems
deseq2 R
updated 4 days ago by 82k • written 5 days ago by • 0
1
vote
2
replies
251
views
POSSUM not working due to incompatible pssm file
fasta pse-pssm pssm POSSUM
4 days ago by rianna.collins • 0
1
vote
0
replies
188
views
News: Landscape Genomics course in Switzerland
LFMM Landscape-Genomics Sambada R Local-Adaptation
4 days ago by carlopecoraro2 ★ 2.5k
1
vote
4
replies
1.1k
views
Filtering qscore on dorado
dorado filtering QC nanopore Guppy
4 days ago by eebloom ▴ 80
1
vote
1
reply
170
views
Super ehancers
enhancers
updated 4 days ago by ★ 16k • written 4 days ago by • 0
1
vote
1
reply
162
views
Download eQTL data of one specific gene for all tissues from GTEx
eQTL GTEx
updated 4 days ago by ★ 2.4k • written 4 days ago by ▴ 20
1
vote
1
reply
138
views
Discrepancy in read counts from fastq
downsampling fastq
updated 4 days ago by 43k • written 4 days ago by ▴ 90
1
vote
3
replies
234
views
DiffBind: no peaks in DBA
MACS2 DiffBind ChIP-seq
updated 3 days ago by ★ 16k • written 3 days ago by ▴ 10
1
vote
14
replies
2.4k
views
Extract gRNA sequence using cutadapt
cutadapt trimming crispr sequencing
updated 3 days ago by 142k • written 4.5 years ago by ▴ 20
1
vote
3
replies
252
views
Bedtools merge minimum overlap?
bedtools genomics
updated 3 days ago by 35k • written 3 days ago by • 0
1
vote
3
replies
280
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 3 days ago by • 0
1
vote
5
replies
329
views
Introduce SNPs on FASTA
simulation snps haplotypes pharmacogenetics
3 days ago by Riccardo ▴ 10
1
vote
3
replies
235
views
Odd alignment question/finding
Alignment
updated 3 days ago by ★ 2.1k • written 4 days ago by • 0
1
vote
7
replies
440
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
2
replies
235
views
RNA-seq data for deep learning classification
rna-seq
3 days ago by yahn • 0
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
1
vote
4
replies
306
views
Segmentation error while using a tool
smalt
updated 2 days ago by ★ 27k • written 2 days ago by • 0
1
vote
1
reply
177
views
DSEQ2 analysis
DESEQ2 logfoldchange
updated 1 day ago by 43k • written 3 days ago by • 0
1
vote
2
replies
225
views
Downloading full alignments from Pfam
pfam
1 day ago by bef1 • 0
1
vote
3
replies
260
views
TaxID mapping file
annotation blobtools RNAseq decontamination transcriptomes
22 hours ago by Lada ▴ 30
1
vote
11
replies
5.5k
views
Truncated Bam Error
R next-gen sequencing software error
updated 12 hours ago by • 0 • written 6.1 years ago by ▴ 20
1
vote
3
replies
278
views
ERROR When Using Ensembl Plants Biomart Wget API
biomart plant ensembl
11 hours ago by Dora ▴ 10
1
vote
10
replies
835
views
error to run rnammer
phylogenomics rRNA_extraction rnammer
updated 9 hours ago by • 0 • written 3 months ago by ▴ 30
1
vote
0
replies
137
views
.lgen file has 3+ different alleles
PLINK lgen ped
updated 8 hours ago by 11k • written 2 days ago by ▴ 10
1
vote
5
replies
207
views
install.packages("imudata") - package ‘imudata’ is not available for this version of R
r
updated 3 hours ago by 43k • written 9 hours ago by • 0
1
vote
5
replies
287
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 2 hours ago by 43k • written 1 day ago by • 0
1
vote
2
replies
77
views
error in R code
R
updated just now by 4.6k • written 5 hours ago by • 0
0
votes
2
replies
154
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified.
DESeq2
updated 4 hours ago by 142k • written 20 hours ago by ▴ 150
0
votes
1
reply
179
views
VG : No reference-sense paths available in the graph; falling back to generic paths.
vg
updated 3 days ago by ▴ 120 • written 3 days ago by • 0
0
votes
0
replies
48
views
News: We created a Bioinformatics Competition for Spatial Transcriptomics: MICOS-EU
cell-clustering Spatial-transcriptomics
updated 3 hours ago by 43k • written 5 hours ago by • 0
0
votes
7
replies
547
views
Post-imputation plot
michigan-imputation-server quality-control
updated 3 days ago by 3.9k • written 6 days ago by ▴ 10
0
votes
0
replies
40
views
Error while loading model of Spatial data deconvolution using cell2location
Python cell2location
updated 3 hours ago by 43k • written 3 hours ago by ▴ 50
0
votes
2
replies
728
views
homer not configured properly
Homer makeTagDirectory
updated 3 days ago by • 0 • written 23 months ago by • 0
0
votes
1
reply
543
views
HOMER on AWS
HOMER
updated 3 days ago by • 0 • written 2.2 years ago by ★ 1.4k
0
votes
0
replies
144
views
SIngle cell analysis
Seurat scRNA-seq Harmony DoubletFinder Merge
3 days ago by Jeyong • 0
0
votes
0
replies
135
views
News: Cellosaurus release 49 is available
cell biocuration line database news knowledgebase
3 days ago by Amos Bairoch ▴ 120
0
votes
5
replies
311
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
0
votes
0
replies
33
views
Normalizing AMR gene count data
abundance RGI
updated 3 hours ago by 43k • written 4 hours ago by ▴ 100
0
votes
5
replies
342
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
0
votes
1
reply
679
views
after selecting specific GO terms to plot, cneplot is not showing any color for genes, GO terms and only showing lines without nodes.
cneplot
updated 5 days ago by 43k • written 5 days ago by • 0
0
votes
2
replies
221
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
27 minutes ago by sovrappensiero ▴ 90
0
votes
0
replies
85
views
Gene ontology and homologs
gene-ontology
updated 3 hours ago by 43k • written 21 hours ago by • 0
0
votes
0
replies
144
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics metacyc enzyme pathway genomics
5 days ago by O.rka ▴ 710
0
votes
0
replies
145
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization illumina ngs sequencing
3 days ago by rustykb ▴ 20
0
votes
2
replies
160
views
Gene Specific coverage from WGS data
linux WGS Bioinformatics SARS CoV2
updated 3 hours ago by 142k • written 6 days ago by • 0
0
votes
0
replies
35
views
16S rRNA microbiome differential abundance analysis with DESeq2 finds same microbial Genus in both groups.
microbiome 16S DESeq2
3 hours ago by Antonio • 0
179 results • Page 2 of 4
Recent Votes
A: Meme-Tools: Bit score
Meme-Tools: Bit score
Meme-Tools: Bit score
Comment: error in R code
DEXSeq multiple time points
How to find the most frequent alternative-splicing event from DEXSEQ data?
Comment: Design matrix Differential expression analysis
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Recent Replies
Comment: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read by kalavattam ▴ 190
Thanks for the explanation. I noticed and corrected a typo in which "*read* reverse strand" initially read as "*mate* reverse strand" in t…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA by sovrappensiero ▴ 90
It's a commercial product, a *Staphylococcus hominis* genome. This species is not found in the DADA2 results, so I guess DADA2 is not ident…
Comment: Question regarding WGCNA by Ram 43k
Plots are incomplete without legends. Please share the complete plot with mappings for shape and color.
Comment: Quetion regarding WGCNA by deepak • 0
Thank you for your reply andres.firrincieli. I have attached the PCA plot of the expression data used in the WGCNA. ![enter imag…
Comment: Design matrix Differential expression analysis by SHN ▴ 40
Got it, thank you for your response. SN
Comment: How to interpret DEXseq results in therms of significance by Sara ▴ 30
Hi, I used write.table(as.data.frame(DEXSeqResults(MyObj)), "Results.tsv", quote=FALSE, sep="\t", dec=".") to save the result but I recei…
Comment: Tissue-specific DEG analysis with DEseq2 by M. ▴ 30
Can I ask what do you exactly mean by same experiment? If you are talking about the same donor and the same procedure, unfortunately, not a…
Comment: install package: package ‘gmwm’ is not available for this version of R by Ram 43k
Find someone with computer skills near you and consult them. From your posts on the forum, it's clear that you need help at a level that we…
Comment: Gene Specific coverage from WGS data by GenoMax 142k
This is not going to work no matter what program you use since the chromosome identifiers in your GTF (`MN908947.3 `) do not match your BA…
Comment: install.packages("imudata") - package ‘imudata’ is not available for this versio by Ram 43k
Read the answers in the post, understand them and try to implement them.
Comment: High Malat-1 expression in single cell data by t.montserrat.ayuso ▴ 10
Just using the normalized expression of Malat1 works.
Comment: Can I merge Hi-C fastq files from different lanes? by Winter • 0
Awesome, thank you for the concise and straight-forward answer!
Comment: error in R code by ATpoint 82k
Look, before you keep posting these sorts of questions and might gross of users, please read and follow https://www.biostars.org/p/357878/ …
Comment: Gene Specific coverage from WGS data by 1769mkc ★ 1.2k
"Also if is there any other quick way to find gene specific coverage" can you give some example so that its bit more clear what do you mean…
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…
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