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780 results • Page 2 of 16
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2
votes
5
replies
365
views
How to calculate TPM from featureCounts output
rna-seq TPM featurecounts
updated 15 hours ago by ▴ 140 • written 2 days ago by • 0
3
votes
10
replies
1.7k
views
6 follow
How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by cell barcode?
10xgenomics RNAseq scRNA CB
updated 1 day ago by ▴ 580 • written 10 months ago by ▴ 20
0
votes
0
replies
76
views
Prediction of altrered metabolites from altered gene expression
Gene Metabolites
1 day ago by english.server ▴ 290
0
votes
3
replies
159
views
CNNScoreVariants Error
CNNscore
updated 1 day ago by 154k • written 1 day ago by ▴ 10
2
votes
1
reply
123
views
Finding Enhancers using Genomation library
Genomation
updated 1 day ago by 72k • written 1 day ago by • 0
0
votes
5
replies
425
views
convert data frame with character column to data frame with integer column
r
updated 1 day ago by ★ 1.6k • written 4 days ago by • 0
0
votes
0
replies
143
views
Pore-C-Snakemake output files
contacts
updated 1 day ago by ▴ 10 • written 6 days ago by • 0
3
votes
3
replies
306
views
Why is coordinate sort required before findng read depths?
wgs sambamba
updated 1 day ago by ▴ 10 • written 4 days ago by • 0
2
votes
2
replies
155
views
how to sort unique seq from fasta files
fasta
updated 1 day ago by 8.1k • written 1 day ago by • 0
2
votes
2
replies
195
views
I need help with a blast command, please help
linux blast
updated 1 day ago by 39k • written 1 day ago by • 0
1
vote
1
reply
154
views
Is there a way to add a transcript to EnsDb.Hsapiens.v86?
ensembldb GenomicFeatures R Bioconducter EnsDb.Hsapiens.v86
1 day ago by Daniel ▴ 30
2
votes
2
replies
151
views
How to make the profile line of `deepTools::plotHeatmap` more smooth?
plotHeatmap deepTools
1 day ago by Dan ▴ 120
0
votes
3
replies
218
views
Convert Bam file to Fastq
Fastq Bam
updated 1 day ago by 39k • written 1 day ago by • 0
0
votes
0
replies
123
views
Job: Data Engineer / Bioinformatician- AZ-Crick-Imperial College: Molecular Glue Discovery Partnership
data-engineering drug-discovery data-science
updated 1 day ago by 39k • written 1 day ago by ▴ 220
0
votes
6
replies
290
views
variant allelic fraction
vep
updated 3 hours ago by 39k • written 1 day ago by • 0
0
votes
2
replies
163
views
WGCNA Trait File Issues
correlation Deseq2 Gene WGCNA
updated 1 day ago by 2.6k • written 1 day ago by • 0
0
votes
1
reply
140
views
Pairwise Alignment
Pairwise-Alignment
updated 1 day ago by 39k • written 1 day ago by • 0
3
votes
6
replies
2.0k
views
h5ad cellxgene to R
single-cell h5 cellxgene anndata R
updated 2 days ago by 129k • written 6 months ago by ★ 1.5k
4
votes
5
replies
322
views
calculate p value and associated z score for snp-gene pair
snp association gene pvalue
updated 23 hours ago by 2.6k • written 4 days ago by ▴ 140
1
vote
3
replies
326
views
What is the benefit of knowing the source of contamination when we have RNAseq data with less than 70% mapping?
alignment mapping STAR contamination RNAseq
1 day ago by Sib ▴ 40
0
votes
0
replies
92
views
How to perform a phylogenetic analysis from a vcf file
variants haplotyping phylogeny vcf
2 days ago by rj.rezwan • 0
0
votes
1
reply
156
views
Where to get the molecular subtype information of STAD sample in TCGA
TCGA database
updated 2 days ago by 2.9k • written 2 days ago by ▴ 50
0
votes
2
replies
225
views
Filtering mitochondrial reads from ATAC-Seq aligned reads- what to do with reads that have MT in RNEXT field
RNEXT filtering mitochondrial_reads ATAC-Seq samtools
updated 1 day ago by 3.6k • written 2 days ago by • 0
1
vote
5
replies
360
views
Is a human genome file with reference as NCBI37 the same as hg19?
vcf hg19 genome reference-genome
updated 2 days ago by 129k • written 2 days ago by • 0
7
votes
4
replies
392
views
Forum: [Meta] Use of AI
AI Artificial-Intelligence meta ChatGPT
updated 1 day ago by 39k • written 2 days ago by ★ 2.9k
0
votes
0
replies
134
views
How to keep ComplexHeatmap from reordering annotations
Dendrogram HeatmapAnnotations R Heatmap ComplexHeatmap
2 days ago by Manuel • 0
3
votes
5
replies
419
views
RNASeq gene labeling and mRNA filter from bulkRNA data.
RNA-Seq RSubreads
updated 15 hours ago by ▴ 140 • written 4 days ago by • 0
1
vote
2
replies
248
views
Random dataset and DESeq2
DESeq2
updated 2 days ago by ★ 2.9k • written 3 days ago by • 0
1
vote
1
reply
215
views
Network cross-validation
wgcna RNASeq Network CV
updated 3 days ago by 2.6k • written 3 days ago by ▴ 500
0
votes
1
reply
166
views
Differential protein expression analysis
R proteomic statistics
updated 7 hours ago by ★ 4.2k • written 3 days ago by ▴ 40
0
votes
3
replies
313
views
(ERR): "index/Trinity.fa" does not exist or is not a Bowtie 2 index Exiting now ...
bowtie2 align_stats trinity
2 days ago by eimanpharmacist ▴ 20
1
vote
2
replies
236
views
I have one fasta file of a bacteria. Can i use to create a phylogenetic tree?
Bioinformatics WGS
3 days ago by Mustafa • 0
0
votes
4
replies
358
views
What are recommended parameters for the local protein alignment ?
protein alignment
2 days ago by Alexander ▴ 70
0
votes
0
replies
126
views
microsatellite, SSR, using Galaxy
Galaxy SSR using microsatellite
3 days ago by m.esmaeilpour ▴ 10
2
votes
2
replies
268
views
integrate single cell RNA sequencing data
scRNAseq single-cell
updated 3 days ago by 2.9k • written 4 days ago by ▴ 50
0
votes
0
replies
142
views
decoupleR & Transcription Factory Activity Inference: pvalue or padj?
pvalue padj decoupleR
3 days ago by OST ▴ 10
3
votes
7
replies
427
views
How to sort gff3 according to chromosome order?
gff3 sort
updated 3 days ago by 154k • written 3 days ago by • 0
2
votes
3
replies
330
views
Low mapping percentage
mapping STAR RNAseq
3 days ago by Sib ▴ 40
0
votes
0
replies
169
views
Visualization App for RNASeq Differential Expression and Enrichment Analysis
differential visualization RNASeq analysis expression enrichment
3 days ago by Mark • 0
4
votes
3
replies
302
views
What does canonical transcript mean in the context of VEP
vep
updated 3 days ago by ★ 2.9k • written 3 days ago by ▴ 720
0
votes
0
replies
188
views
Job: Postdoctoral Research Associate in bio-ontologies and machine learning (Imageomics)
Machine-Learning PostDoc Data-Science Biology Ontology
updated 3 days ago by 39k • written 4 days ago by • 0
3
votes
4
replies
289
views
bcftools "--filter-logic" flag, what + means?
bcftools vcf
updated 1 day ago by ▴ 360 • written 4 days ago by ▴ 170
0
votes
0
replies
156
views
busco id description
OrthoDB BUSCO
updated 4 days ago by 39k • written 4 days ago by • 0
0
votes
5
replies
379
views
how to Construct a Newick tree file from five large fasta files
tree Newick alignment
updated 3 days ago by 21k • written 4 days ago by • 0
2
votes
7
replies
492
views
What is "pident" (percentage of identical matches) in the "Diamond" protein alignment ?
protein alignment
updated 3 days ago by ★ 2.9k • written 4 days ago by ▴ 70
0
votes
0
replies
162
views
NMDS plotting issue
NMDS metagenomic
4 days ago by arshad1292 ▴ 90
0
votes
2
replies
231
views
featurecounts not working on mirbase annotation file
usegalaxy miRNA-seq
22 hours ago by demoraesdiogo2017 ▴ 90
0
votes
0
replies
155
views
News: Generalized Linear Models (GLM) course in R
R GLM statistics
4 days ago by carlopecoraro2 ★ 2.3k
0
votes
0
replies
138
views
IGV insertions
insertions IGV
4 days ago by christoph.schubart • 0
1
vote
0
replies
150
views
Bayesian network for biological data using bnlearn
bnlearn RNA-seq bayesian-network
updated 4 days ago by 39k • written 4 days ago by ▴ 10
780 results • Page 2 of 16
Recent Votes
Calculating read abundances across MAGs (question)
Comment: Contigs to chromosomes annotation
Comment: Contigs to chromosomes annotation
Comment: Same GEO Accession, different SRR number, how to download this RNA-seq paired-en
Comment: Same GEO Accession, different SRR number, how to download this RNA-seq paired-en
Answer: how to choose an efficient filtering threshold to remove shorter and low quality
Contigs to chromosomes annotation
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Recent Replies
Comment: Diff Bind Questions by Ram 39k
I've moved this to a comment as it does not directly answer OP's question.
Comment: Diff Bind Questions by Daniel ▴ 30
I'm very new myself and there's plenty of people who can answer your question better than I can, but here is a resource I found extremely h…
Comment: Contigs to chromosomes annotation by alexandru.bologa.marian ▴ 50
If the number of contigs was so small I would manually check each alignment and edit the header of each contig,inserting the corresponding …
Comment: Gviz Coverage Plots by Ram 39k
Do not post on multiple fora just because you want a fast response, it's plain rude. At least point to the other post so we know you're ask…
Comment: Limma returned only positive logFC values by melissachua90 ▴ 40
No the library sizes across conditions should be relatively homogenous because it's from the same dataset. I clustered the samples into sub…
Comment: Limma returned only positive logFC values by LChart 2.6k
It shouldn't, unless there's a misspecification in design. Is it the case that the library sizes are very different between the conditions …
Comment: Contigs to chromosomes annotation by Darked89 4.3k
For a pure contig to Dmel chromosome BLAST should be OK. I am fan of LAST because it is fairly easy to convert MAF to SAM/BAM and then vi…
Comment: Contigs to chromosomes annotation by GenoMax 129k
How many contigs do you have? If the contigs are ~2x number of Drosophila chromosomes (meaning you have long/large contigs) then using a lo…
Comment: Contigs to chromosomes annotation by alexandru.bologa.marian ▴ 50
Thank you for your answer! It would be wrong just to BLAST all the contigs from the draft assembly against each reference chromosome of D.…
Comment: Limma returned only positive logFC values by melissachua90 ▴ 40
Several hundred to 10000 DEGs. Would normalization affect logFC?
Answer: Contigs to chromosomes annotation by Darked89 4.3k
Not sure if it is the easiest, but you can map your new assembly to i.e. Dmel genome using LAST: * www: https://gitlab.com/mcfrith/last …
Answer: Gene prediction software by Darked89 4.3k
How complete/polished is your catfish genome assembly? Also: do you have some good quality RNA-Seq? With a draft genome it would be…
Comment: Limma returned only positive logFC values by LChart 2.6k
It'd be helpful to know how many differentially expressed genes there are. If you've got a handful and they're all upregulated, I wouldn't …
Comment: variant allelic fraction by Ram 39k
Cross-posted on bioinfo SE: https://bioinformatics.stackexchange.com/questions/21118/how-to-calculate-the-variant-allelic-fraction-vaf OP,…
Comment: Same GEO Accession, different SRR number, how to download this RNA-seq paired-en by GenoMax 129k
You can `cat` the respective R1/R2 files in same order e.g. `cat Run1_R1.fq.gz Run2_R1.fq.gz > R1.fq.gz`.
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