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How to compare two datasets of proteomic analysis when there are unique and common proteins?
proteomics mass spectrometry protein replication
4.6 years ago by Farah ▴ 80
0
votes
3
replies
1.7k
views
top geo ontology
RNA-Seq
4.6 years ago by aranyak111 • 0
2
votes
1
reply
3.1k
views
BOLD systems database for qiime?
qiime BOLD
updated 4.6 years ago by 20 • written 8.8 years ago by ▴ 870
1
vote
2
replies
1.6k
views
plotting the tree in XGBoost
XGBoost
updated 2.5 years ago by 45k • written 4.6 years ago by ▴ 80
0
votes
2
replies
1.6k
views
Error occur during tophat2 downloading
tophat2 make
updated 4.6 years ago by 13k • written 4.6 years ago by ▴ 40
0
votes
0
replies
893
views
Cox regression on Splicing. PSI in 0 to 1 or 0 to 100 range
cox RNA-Seq
4.6 years ago by mario.keller1988 • 0
4
votes
4
replies
1.5k
views
How do I remove Batch Effects from Two Separate raw RNA SEQ datasets
RNA-Seq comBat-seq datasets
4.6 years ago by merfer0206 • 0
0
votes
1
reply
1.9k
views
TrimGalore! not properly removing low quality base calls.
RNA-Seq
updated 4.6 years ago by 20 • written 4.6 years ago by • 0
4
votes
4
replies
1.2k
views
Forum: Looking for a CS PhD Program + tips
PhD
updated 2.5 years ago by 45k • written 4.6 years ago by • 0
2
votes
2
replies
3.2k
views
How to deal with the issue when STRING database could not find a protein, or instead matched its similar protein?
proteomics STRING interaction network uniprot
updated 4.6 years ago by ▴ 80 • written 4.6 years ago by ▴ 80
1
vote
1
reply
1.1k
views
How could I change the transparency of the a density plot in ggpairs function (GGally)
R software error
updated 4.6 years ago by 89k • written 4.6 years ago by • 0
29
votes
4
replies
9.7k
views
Forum: Update to tbb (2021.1.1, conda-forge) breaks bowtie2 (bioconda)
software-error bowtie2 bioconda conda tbb
updated 2.5 years ago by 45k • written 4.6 years ago by ▴ 240
1
vote
2
replies
895
views
Gene expression and chromatin state
DNA expression chromatin
4.6 years ago by whb ▴ 60
0
votes
3
replies
1.2k
views
Alignment: how to deal with read mapped on decoy
alignment genome
updated 4.3 years ago by ▴ 60 • written 4.6 years ago by ▴ 120
0
votes
0
replies
1.2k
views
Nanopolish makerange for smaller contigs
assembly genome
4.6 years ago by SUDOsundu ▴ 80
3
votes
3
replies
7.5k
views
VCFTOOLS --recode and --recode-INFO-all
SNP gene vcf
updated 4.6 years ago by 20 • written 7.4 years ago by ▴ 250
0
votes
3
replies
1.1k
views
Query regarding variant calling and reporting
clinical exome whole exome compound heterozygous
4.6 years ago by luffy ▴ 130
0
votes
1
reply
1.1k
views
Biopython byte positions are not compatible with bgzip
htslib biopython bgzip
updated 4.6 years ago by ★ 2.0k • written 4.6 years ago by • 0
3
votes
3
replies
4.1k
views
Error in y - mu : non-numeric argument to binary operator - linear regression loop
bulkRNAseq R linear regression
updated 4.6 years ago by ★ 4.8k • written 4.6 years ago by ▴ 160
2
votes
3
replies
1.8k
views
Medaka tools annotation missing QUAL values
haploid medaka variant-calling nanopore
updated 23 months ago by 45k • written 4.6 years ago by ▴ 80
0
votes
0
replies
669
views
Does anyone succeded clustering TCGA data?
RNA-Seq TCGA clustering
updated 4.6 years ago by 20 • written 4.6 years ago by • 0
0
votes
3
replies
2.7k
views
Bowtie2 to map multiple fastq.gz files?
bowtie2 for loop
4.6 years ago by karlitavasco87 • 0
0
votes
4
replies
1.2k
views
Finding gene of interest in data downloaded from SRA
SRA RNA-Seq
updated 4.6 years ago by ★ 3.9k • written 4.6 years ago by • 0
2
votes
5
replies
3.7k
views
In blasp their is %identity? how to find similarity percentage in blastP ??
sequencing
updated 2.3 years ago by 45k • written 7.1 years ago by • 0
1
vote
5
replies
1.7k
views
GATK VCF output: where are the sample-level annotations?
SNP sequence GATK VCF
4.6 years ago by mcrepeau ▴ 20
4
votes
5
replies
1.7k
views
Extracting CDS from fragmented assemblies
Assembly alignment
updated 4.6 years ago by ★ 3.3k • written 4.6 years ago by ▴ 40
3
votes
1
reply
1.7k
views
Tool: Introducing Gallia: a Scala library for data manipulation
scala etl json vcf spark
updated 2.3 years ago by 45k • written 4.6 years ago by ▴ 30
2
votes
3
replies
3.6k
views
choose specific python version within conda environment
conda python
4.6 years ago by AQ7 ▴ 30
0
votes
1
reply
910
views
bwa read group tagging failed in PBS cluster
alignment next-gen software error
updated 4.6 years ago by 20 • written 4.7 years ago by ▴ 10
1
vote
0
replies
1.1k
views
Correct Data from TCGA for EdgeR Analysis
rna-seq
4.6 years ago by joseph.landry ▴ 50
1
vote
5
replies
2.2k
views
Reading multiple txt files and perform Two Sample Mendelian Randomization in R
2 sample MR Multiple txt files
4.6 years ago by mscpythonstudy ▴ 20
0
votes
5
replies
2.3k
views
Creating Correlation Plot using distance method from a data.frame
R correlation corrplot
updated 4.6 years ago by ★ 30k • written 4.6 years ago by • 0
0
votes
0
replies
668
views
Finding mutational burden in TCGA dataset
genome python UTR tcga cancer
4.6 years ago by Jamie Watson ▴ 10
4
votes
5
replies
4.3k
views
Replace fasta Header witha a matching text
awk seqkit grep
updated 4.6 years ago by 153k • written 4.6 years ago by ▴ 190
0
votes
0
replies
695
views
rmsd graph equilibrium
MD Simulation rmsd
4.6 years ago by prinebula23 • 0
0
votes
1
reply
559
views
Error while running the transcript count file obtained using StringTie on DeSeq2
R sequencing software error
4.6 years ago by vedant23081998 • 0
2
votes
4
replies
1.5k
views
Isoform detection of a gene using RNAseq
RNA-Seq isoform_detection
4.6 years ago by vinishavvenugopal ▴ 30
0
votes
0
replies
631
views
ViewBS error in visualizing BSSeq data
Bisulfite sequencing Analysis software error
updated 4.6 years ago by 153k • written 4.6 years ago by ▴ 10
0
votes
1
reply
787
views
Extract features from fasta sequences
fasta feature-extraction machine-learning
4.6 years ago by suresh.wrc • 0
6
votes
4
replies
5.2k
views
Forum: Chip-Seq Data Analysis
chip-seq
updated 2.6 years ago by 45k • written 13.4 years ago by ★ 1.5k
9
votes
10
replies
20k
views
6 follow
GO analysis- analyze upregulated and downregulated genes separately?
RNA-Seq
updated 3.0 years ago by 45k • written 10.1 years ago by ▴ 30
3
votes
2
replies
1.1k
views
Job: Need Transcriptome bioinformatician's collaboration
next-gen-sequencing R RNA-seq alignment
updated 2.3 years ago by 45k • written 4.6 years ago by ▴ 20
35
votes
22
replies
25k
views
13 follow
Renaming fasta headers according to a matching name list
text-processing command-line sequence
updated 3.5 years ago by ▴ 20 • written 9.5 years ago by ▴ 190
3
votes
2
replies
910
views
Order a chromsome assembly with a chromosome assembly of a closely related species/
assembly genome
updated 4.6 years ago by 15k • written 4.6 years ago by ▴ 10
2
votes
3
replies
2.4k
views
Deeptools plotHeatmap values
Deeptools plotHeatmap ChIP-Seq
updated 2.3 years ago by 45k • written 4.6 years ago by • 0
1
vote
6
replies
2.0k
views
GATK issue in running Mutect2
next-gen snp
updated 4.6 years ago by ▴ 350 • written 4.7 years ago by • 0
7
votes
9
replies
9.7k
views
6 follow
Getting mitochondrial genes for scRNAseq
RNA-Seq rna-seq scRNAseq single-cell
updated 4.6 years ago by ▴ 10 • written 5.2 years ago by • 0
1
vote
4
replies
2.0k
views
Correspondence between unlabeled/different tips of different phylogenetic trees
Phylogenetics Trees gene sequence
updated 4.6 years ago by 20 • written 7.6 years ago by • 0
0
votes
0
replies
630
views
lncRNA-target reference file with proper gene nomenclature
gene genome-sequencing lincRNA
updated 2.5 years ago by 45k • written 4.6 years ago by ▴ 320
0
votes
1
reply
795
views
Getting ENTREZ GENE IDs for data frame, any help?
R gene Assembly
updated 4.6 years ago by 21k • written 4.6 years ago by • 0
121,914 results • Page 702 of 2439
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Comment: Variant analysis for mouse WES
Comment: Why is academic software hard to install?
A: Concatenate multiple MUSCLE alignment result to build a phylogenetic tree
Comment: Different UMAP for batch correction in R and Pytho
Getting VCF file for the 1000 genome project with rsid
Answer: Different UMAP for batch correction in R and Pytho
Answer: Different UMAP for batch correction in R and Pytho
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Recent Replies
Answer: Genome Assembly QC from BAM files by colindaven 7.9k
You can have a look at the tools in the PAQman pipeline https://github.com/SAMtoBAM/PAQman, and maybe also Inspector https://github.com/Mag…
Comment: [vg giraffe] Unable to add read group to BAM file by Arup Ghosh 3.4k
I didn't find any documentation related to the formatting, but it seems `vg` only supports strings in the following format. The BWA style y…
Comment: Concatenate multiple MUSCLE alignment result to build a phylogenetic tree by san96 ▴ 190
Hi Mensur, sorry for this but I'm a little stuck. I’m trying to build a species tree for the first time and I would like to clarify a few …
Comment: Tried building a compact sequence format with 4-bit storage by Alex Reynolds 36k
In addition to looking at other tools as a baseline: https://en.wikipedia.org/wiki/Compression_of_genomic_sequencing_data maybe also look i…
Comment: Different UMAP for batch correction in R and Pytho by Madiha ▴ 20
Thanks, António for a helpful, detailed response. I didn't take into consideration that the plotting order of cells from each batch can be …
Comment: [vg giraffe] Unable to add read group to BAM file by saruman • 0
It seems that using the following format fixes the problem: --read-group "1 SM:HG002 LB:lib1 PL:illumina PU:unit1" As shown below: …
Comment: Developing a genomics ML model using bytes? by dariober 15k
> what if we can use the bytes to develop a model? My understanding is that the OP is considering building a model using the sequences in …
Comment: WGCNA package in R: dendogram plot error by RJ • 0
You might had delete the outliers from the expression table but then the traits data.frame doesn't match with expression table dimensions.
Comment: miRNA low mapping ratings by Ant ▴ 50
No, it's a personal dataset. I haven’t seen the link, but if I understand correctly, it's not possible to use the software for free, right?
Comment: miRNA low mapping ratings by GenoMax 153k
So this is a public dataset? QIAseq miRNA libraries may require special handling. Have you seen --> https://resources.qiagenbioinformatics.…
Comment: Trouble when installing arb by GenoMax 153k
Are you referring to software found here --> http://download.arb-home.de/release/latest/ ? If so why are you installing the source. Authors…
Comment: Hifiasm is getting killed while trying to assemble a genome by GenoMax 153k
All valid points. This is a SRA dataset. If it is covered by a publication hopefully it is not a bad one. @Pranav if you can post the SRA a…
Answer: Different UMAP for batch correction in R and Pytho by antonioggsousa 3.4k
Hi, I'm mostly an R user, but the codes you presented look correct to me. The two UMAP projections *"look too similar to be different"*, …
Answer: How to properly assemble phage genomes? by Joe 22k
This might help: https://millardlab.org/lab-members/alumni/lucy-gannon/lucys-beginner-guide-to-bacteriophage-genome-assembly/
Comment: RNA-SEQ where only a subset of genes is of interest by piffelpaff • 0
Thanks for your reply. Yes it's single-cell and we're talking about roughly 30 pre-selected genes. I see. I was rather referring to the d…
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