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4
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2.3k
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GISTIC installation error
GISTIC2.0 CNV GISTIC
updated 4.4 years ago by 5.9k • written 4.4 years ago by ▴ 10
0
votes
2
replies
3.0k
views
How to get uniprot ID or protein length from Entrez gene id or gene name?
panther python David uniprot API
4.4 years ago by eranga114 • 0
0
votes
1
reply
1.7k
views
Job: Bioinformatics Training Specialist, HDC
Seattle
updated 4.4 years ago by 45k • written 4.4 years ago by ▴ 30
4
votes
4
replies
1.7k
views
How to perform alternative splicing from RNA Seq data?
RNA-Seq alternative-splicing
updated 4.4 years ago by 45k • written 4.4 years ago by ▴ 50
3
votes
2
replies
3.7k
views
What are the makeblastdb database files doing?
blastp database
4.4 years ago by timothy.kirkwood ▴ 140
1
vote
0
replies
779
views
Removing paralogs from multiple sequence alignments
sequencing BAM genomics comparative paralog
4.4 years ago by mglasena ▴ 40
0
votes
0
replies
737
views
Splitting predicted transcripts according to ORF coordinates
transcript ORF RNAseq
4.4 years ago by Buffo ★ 2.5k
3
votes
5
replies
1.8k
views
Collecting CDS from transcripts using Entrez
entrez biopython
updated 4.4 years ago by 154k • written 4.4 years ago by • 0
3
votes
6
replies
2.7k
views
how to align fastq files to a fasta file using biopython to produce VCF file
fastq biopython fasta VCF
updated 4.4 years ago by 45k • written 4.4 years ago by ▴ 20
2
votes
5
replies
1.6k
views
how to determine genes expressed in NK cells using DE RNA-Seq data
ImmGen NKcellgenes
updated 4.4 years ago by 45k • written 4.4 years ago by ▴ 40
3
votes
3
replies
3.6k
views
scRNAseq analysis with logNormCounts (scran/scuttle package) - log transformation with different log base?
scran log logNormCounts scuttle scRNAseq
updated 4.4 years ago by 90k • written 4.4 years ago by ▴ 150
0
votes
0
replies
1.4k
views
How not to overlap statistical symbols (asterisks) on a comparison with multiple groups boxplot (ggplot2) ?
asterisks ggplot2 boxplot stats multiplegroups
4.4 years ago by LuisNagano ▴ 90
0
votes
2
replies
1.0k
views
Differential expression analysis
DEGs
updated 4.4 years ago by ▴ 390 • written 4.4 years ago by • 0
7
votes
9
replies
6.7k
views
Volcano plot from a RNAseq excel file
Volcanoplot
updated 4.4 years ago by 45k • written 4.4 years ago by • 0
0
votes
0
replies
816
views
p.value of Fst calculate with snpgdsFst
snpgdsFst Fst
updated 4.4 years ago by 45k • written 4.4 years ago by • 0
0
votes
4
replies
2.0k
views
how to align many single end fastq files from the same study on each other without using any reference genome using python?
fastq fasta python VCF
updated 4.4 years ago by 154k • written 4.4 years ago by ▴ 20
2
votes
1
reply
4.2k
views
Normalization after merging Seurat objects
Seq Seurat ScRNA-Seq RNA
updated 4.4 years ago by ★ 1.8k • written 4.4 years ago by ▴ 40
1
vote
6
replies
2.8k
views
convert Ensemble to HGNC symbols in a file with several columns
mariadb
4.4 years ago by storm1907 ▴ 30
0
votes
7
replies
2.1k
views
Ensembl Highlighted Exons Don't Match Coordinates
ensembl
updated 4.4 years ago by 24k • written 4.4 years ago by ▴ 840
3
votes
5
replies
1.7k
views
Biopython DSSP "unexpected sidechain number" Warning
PDB Biopython DSSP
4.4 years ago by sajid ▴ 20
0
votes
0
replies
1.1k
views
Treemix showing "ERROR: CH-JL does not have two alleles (expecting SNP data)"
Population SNP geneflow Treemix genetics
4.4 years ago by virtualinterlect • 0
0
votes
0
replies
640
views
Differential analysis on RNA-seq : Different results with two "equivalent" contrast matrix
design contrast rna-seq
updated 4.4 years ago by 22k • written 4.4 years ago by • 0
0
votes
1
reply
2.0k
views
Adding multiple RG values in Bowtie2 when aligning with multiple fastq
fastq group bowtie2 read
4.4 years ago by Runscar • 0
2
votes
2
replies
1.0k
views
Nr database storage issues
blast database
updated 4.4 years ago by ★ 30k • written 4.4 years ago by ▴ 70
0
votes
2
replies
935
views
SolGenomics IDs to EnsembleGENEid gene list?
gene id
4.4 years ago by manekineko ▴ 10
0
votes
4
replies
2.0k
views
Converting multiple cram files to fastq files.
cram fatsq
updated 4.4 years ago by 45k • written 4.4 years ago by • 0
1
vote
3
replies
2.5k
views
igvtools not running, issue with java
igv jdk igvtools java
4.4 years ago by williamtmills ▴ 20
2
votes
3
replies
1.7k
views
Convert BAM files to FastQ
fastq bedtools samtools bam
updated 4.4 years ago by 15k • written 4.4 years ago by ▴ 10
7
votes
11
replies
3.5k
views
6 follow
how to convert to computational biology from bioinformatics
software computational-biology algorithm
updated 2.7 years ago by 45k • written 4.4 years ago by • 0
0
votes
0
replies
751
views
HTseq low counts
snakemake RNASeq htseq
4.4 years ago by aka ▴ 10
0
votes
0
replies
1.5k
views
Split Y-Axis of a manhattan plot in qqman (using R)
manhattan R genomics
4.4 years ago by tacrolimus ▴ 150
3
votes
3
replies
1.2k
views
Why split fastq files?
fastq alignments ngs bwa
updated 4.4 years ago by 154k • written 4.4 years ago by ▴ 70
0
votes
0
replies
1.3k
views
How to get transcript level estimates in TPM from TCGA BRCA
RNA-Seq BRCA TCGA
4.4 years ago by StartR ▴ 30
0
votes
3
replies
2.5k
views
GNU plot problem
psmc bash
4.4 years ago by gubrins ▴ 350
0
votes
2
replies
1.4k
views
CPM and FPKM for machine learning
RNA-seq
updated 4.4 years ago by 11k • written 4.4 years ago by ▴ 60
1
vote
6
replies
2.9k
views
biomaRt does not convert entrez gene id to ensembl gene id
biomaRt ensembl entrez NCBI
updated 4.1 years ago by ★ 2.1k • written 4.4 years ago by ▴ 30
2
votes
8
replies
2.4k
views
GC content of specific regular expression
GC-content
updated 16 months ago by 45k • written 4.4 years ago by ▴ 10
0
votes
5
replies
1.6k
views
Samtools Flagstat Comments
Samtools BAM Rna-Seq Alignment
updated 4.4 years ago by 154k • written 4.4 years ago by ▴ 40
0
votes
0
replies
1.9k
views
Job: PhD scholarship in Yeast Metabolic Engineering
Metabolic RNAseq Engineering proteomics DNAseq
4.4 years ago by info ▴ 90
1
vote
5
replies
2.5k
views
Install Kent Source Archive Binaries
faToTwoBit
4.4 years ago by kacollier ▴ 30
0
votes
1
reply
983
views
Single-cell atlas
rnaseq singlecell seurat
updated 4.4 years ago by ★ 19k • written 4.4 years ago by ▴ 20
0
votes
4
replies
3.6k
views
the relationship of ATAC-seq and H3K27ac
and ChIP-seq ATAC-seq
4.4 years ago by biohubx • 0
0
votes
0
replies
762
views
Visualization of the cell cycle for ESC (or iPSC) from scRNA-seq data
cell cycle ESC
4.4 years ago by Alexander ▴ 220
0
votes
0
replies
1.9k
views
How to index a genome.gff file? SNPcalling
snp artemis tabix prokka gff
updated 4.4 years ago by 90k • written 4.4 years ago by • 0
3
votes
2
replies
1.7k
views
gVCF size human genome
variant Gatk gvcf
4.4 years ago by quentin54520 ▴ 120
0
votes
1
reply
1.0k
views
Adding insect abundance data to SparCC Analysis
Microbiome metagenomics 16S microbiome SparCC
updated 4.4 years ago by ★ 90k • written 4.4 years ago by ▴ 10
4
votes
4
replies
2.4k
views
setting genotypes to missing
genotype vcf impute
4.4 years ago by raalsuwaidi ▴ 110
2
votes
2
replies
1.4k
views
Unknown trimmer, paired end, other solutions not working
trimmomatic software error
updated 4.4 years ago by 154k • written 4.4 years ago by • 0
0
votes
2
replies
1.1k
views
Needle error - cannot get second filename
needle bash
4.4 years ago by kaixas • 0
3
votes
1
reply
8.3k
views
What is the difference between covariate with fixed effect and random effect?
covariate mlm componentsvariance gwas
updated 4.4 years ago by ▴ 130 • written 4.4 years ago by ▴ 50
122,199 results • Page 629 of 2444
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Answer: Can i use orthofinder for small protein datasets and not full proteome?
Comment: Comparison of different RNAseq data sets
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Comment: low quality data or file name swapping -- cellranger arc errors when processing by Arup Ghosh 3.5k
You can check the read lengths of each file to determine which one is the R1 and which is the R2. Also, check the 10x protocol version they…
Comment: Subsetting before QC in Spatial Transcriptomics by Kent ▴ 30
Hi Kevin, Thanks for the detailed explanation. Due to the characteristics of the datasets, we initially used very lenient quality control…
Comment: Midpoint rooting IQTREE newick file moves node support around by Luca Arbore ▴ 10
Thank you very much Kevin, it worked!
Comment: ID unifiying across different datasets by GenoMax 154k
In this case the entry notes that this is likely the product of a pseudogene: https://www.uniprot.org/uniprotkb/Q5VTE0/entry and existence …
Comment: Comparison of different RNAseq data sets by DrSmad ▴ 10
Each lab contributes both control and LPS. Example, for cell line A_lab1 did and analysis on control and LPS-6h. Cell line B_lab2 did contr…
Comment: ID unifiying across different datasets by zizigolu ★ 4.4k
sorry, why some gene names are often lacking though the Uniprot ID is still valid (using biomart)?
Comment: snpEff: Unsupported structural variant types by shpak.max ▴ 70
Unfortunately, while it ran without a problem initially, when I checked the run screen today, I saw the following error message (and unlike…
Comment: ID unifiying across different datasets by GenoMax 154k
You can use the [**ID mapping tool**][1] from UniProt site (third ID did not map from the list above): From To P68104 ENSG0000015…
Answer: The geo samples is not having sentrix id and sentrix position. But this informat by yura.grabovska ▴ 890
Crosspost from related question: https://www.biostars.org/p/9616466/#9616534 ``` ##Using R, illuminaio from Bioconductor library(…
Answer: Finding Sentrix ID in HM450K arrays by yura.grabovska ▴ 890
``` ##Using R, illuminaio from Bioconductor library(illuminaio) temp.idat <- readIDAT(file = "200379120087_R02C02_Grn.idat") tem…
Comment: Can i use orthofinder for small protein datasets and not full proteome? by michael.ante ★ 4.0k
Do you want to compare them by sequence or by function? For the later, you can use e.g. InterProScan, KoFamScan.
Answer: Can i use orthofinder for small protein datasets and not full proteome? by dthorbur ★ 3.2k
If you're just using the tool for clustering purposes, I think OrthoFinder might be a little clunky and would recommend using something lik…
Comment: ID unifiying across different datasets by zizigolu ★ 4.4k
Thank you; The problem is let's say in the protein ID column I see `Q5VTE0;P68104;Q05639` here I am sure I should get which `ENSG` for eac…
Comment: How to improving 2-Nucleotide RNA-seq Mapping Accuracy by 2411110159 • 0
Since we do not have real data yet, I tried to simulate this using strand-specific RNA bisulfite-seq reads (C to T). Read1 corresponds to t…
Comment: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies by 2411110159 • 0
Very helpful!
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