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1.1k
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Export ensembl efetch in comma-delimited format
format efetch ensembl
updated 4.4 years ago by 153k • written 4.4 years ago by ▴ 760
0
votes
5
replies
1.8k
views
Merging two linux files based on same rows
rsID coordinates plinkfile Merge
updated 4.4 years ago by 153k • written 4.4 years ago by ▴ 70
0
votes
0
replies
756
views
Job: Senior Staff Bioinformatician at the University of Melbourne Centre for Cancer Research
cancer genomics
4.4 years ago by Oliver • 0
47
votes
12
replies
42k
views
9 follow
What is a gene transcript?
sequencing ensembl gene transcript
updated 4.4 years ago by • 0 • written 8.5 years ago by ▴ 110
0
votes
1
reply
874
views
Chosing a phylogenetic tree construction method
tree phylogenetic method
updated 4.4 years ago by ▴ 120 • written 4.4 years ago by ▴ 170
0
votes
1
reply
1.6k
views
error in snakemake
gatk snakemake
updated 4.4 years ago by 21k • written 4.4 years ago by ▴ 100
0
votes
0
replies
563
views
Role of the 'Known resource' in VQSR
GATK gatk VariantRecalibrator VQSR
4.4 years ago by SBM_Han • 0
2
votes
4
replies
2.7k
views
Looping in R to perform a GSEA analysis
RNA-Seq GSEA loops R
updated 4.4 years ago by 89k • written 4.9 years ago by ▴ 390
1
vote
2
replies
1.1k
views
bedtools error
bedtools bash
updated 4.4 years ago by 89k • written 4.4 years ago by • 0
0
votes
4
replies
1.5k
views
How to read a series matrix into R
R GEO seriesmatrix Expressionmatrix
4.4 years ago by waveafterwave • 0
0
votes
0
replies
693
views
PAML/CODEML: which sites are selected in site model?
paml codeml
4.4 years ago by DNAlias ▴ 40
2
votes
2
replies
1.8k
views
DNA vs RNA seq for microbiome
microbiome rnaseq sequencing
updated 4.4 years ago by ★ 2.2k • written 4.4 years ago by ▴ 120
0
votes
0
replies
734
views
What size regions to use for motif Identification from differential H3K27ac peaks ?
H3K27ac homer motif
4.4 years ago by gkunz ▴ 30
2
votes
2
replies
1.8k
views
how to find different expressed genes in GEO2R and do I have to apply a process to the results I get from GEO2R
genes venn expressed different GEO2R
4.4 years ago by eckmk ▴ 10
6
votes
12
replies
17k
views
11 follow
Forum: Online/remote/distance learning/ - partime/fulltime - PhD, Bioinformatics in USA
PhD university
updated 2.5 years ago by 45k • written 9.0 years ago by ▴ 20
1
vote
5
replies
2.4k
views
hisat2 error
hpc hisat2
updated 4.4 years ago by 45k • written 4.4 years ago by ▴ 40
0
votes
4
replies
2.4k
views
biomart returns several ensembl ids for one gene
scrna-seq ensembl biomart r
4.4 years ago by fifty_fifty ▴ 90
0
votes
2
replies
980
views
Clustering 10X scRNA data based on selected markers
clustering scRNA seurat umap pca
4.4 years ago by A • 0
0
votes
0
replies
609
views
KeyError in the pipeline SECAPR
SECAPR Hyb-Seq locus_selection Python Key_error
4.4 years ago by Begonia_pavonina ▴ 210
2
votes
1
reply
600
views
Compatilibity between human37 and human38 gtf
GRCh37v75
updated 4.4 years ago by 48k • written 4.4 years ago by ▴ 70
0
votes
0
replies
2.8k
views
Question about FindMarkers avg_logFC and how to get all features from an assay
seurat singlecell Seurat
4.4 years ago by compuTE ▴ 140
8
votes
8
replies
2.6k
views
6 follow
DESeq2 adjusted p-values of 0 when p-value > 0.05
RNA-seq DEseq2
updated 4.4 years ago by ▴ 390 • written 4.4 years ago by • 0
0
votes
0
replies
540
views
How to calculate the weighted average for each linkage group?
QTLMapping Genetics
4.4 years ago by wkmustahs21 ▴ 30
1
vote
4
replies
2.3k
views
Prefetch not working for SRA
SRA prefetch
updated 4.4 years ago by 153k • written 4.4 years ago by • 0
0
votes
0
replies
603
views
Job: Evolutionary and anthropological genomics postdoctoral fellow at University at Buffalo
Evolution Anthropology Transcriptomics Genomics
4.4 years ago by Omer • 0
0
votes
3
replies
1.2k
views
Gene filtering returns NULL dimensions
R filtering affymetrix genefilter CEL
4.4 years ago by purestdata • 0
0
votes
4
replies
1.3k
views
Very low alignment rate for miRNAs reads against known miRNAs from mirbase
smRNA
updated 4.4 years ago by 23k • written 4.4 years ago by • 0
1
vote
5
replies
1.6k
views
How to ID cell types using reference scRNAseq dataset
Seurat groups scRNAseq
4.4 years ago by FantasticAI ▴ 60
3
votes
1
reply
764
views
Criteria for classifying circular sequences
genome GenBank circular sequence
updated 4.4 years ago by ★ 30k • written 4.4 years ago by ▴ 10
1
vote
1
reply
788
views
How to overcome issue linked to loading big R object
R methylation bioconductor minfi
4.4 years ago by Fede_Santos95 ▴ 20
0
votes
2
replies
1.2k
views
Make info tag separate column VCF
vcf ANGSD
updated 4.4 years ago by 45k • written 4.4 years ago by ▴ 20
3
votes
1
reply
6.6k
views
When use enricher function or GSEA of clusterProfiler R
GSEA enricher genes enrichment clusterProfiler
updated 4.4 years ago by 35k • written 4.4 years ago by ▴ 20
1
vote
4
replies
1.6k
views
Blast Output with only one line
blast
4.4 years ago by pablo ▴ 350
1
vote
3
replies
1.3k
views
Use BCBio package
windows Python3.9
updated 4.4 years ago by 45k • written 4.4 years ago by ▴ 80
2
votes
3
replies
1.3k
views
Mitochondrial genes filtration
scRNA-Seq
updated 4.4 years ago by 89k • written 4.4 years ago by • 0
0
votes
3
replies
3.6k
views
Where to get genetic map build 38 ?
genome next-gen
updated 4.4 years ago by • 0 • written 7.3 years ago by ▴ 350
3
votes
8
replies
2.0k
views
how to order values with different classes in R
R order
4.4 years ago by szp770 ▴ 10
1
vote
2
replies
1.2k
views
Getting Null in sink file when running lme in R using python to generate multiple R codes
R python lme sink
updated 4.4 years ago by 45k • written 4.4 years ago by ▴ 70
0
votes
0
replies
644
views
GATK VariantEval no concordance between dbSNP and our data
VariantEval GATK dbSNP Percentage
4.4 years ago by Pierre_Bioinfo • 0
5
votes
3
replies
1.4k
views
Where I can get the gtf file of antheraea mylitta
GTF
updated 4.4 years ago by 15k • written 4.4 years ago by ▴ 80
0
votes
4
replies
1.3k
views
How to merge genomic features shared by more than one samples
bedtools gene RNA-seq bed annotation
4.4 years ago by tianshenbio ▴ 190
0
votes
5
replies
2.4k
views
substance BxH
WGCNA
updated 4.4 years ago by 89k • written 4.4 years ago by • 0
0
votes
0
replies
739
views
Tool for list protein mutation sites from WT/variants sequences
Mutations Protein
updated 2.3 years ago by 45k • written 4.4 years ago by • 0
0
votes
0
replies
795
views
Extracting the genes associated drugs?
bank Drug
4.4 years ago by mathavanbioinfo ▴ 80
2
votes
2
replies
1.2k
views
Remove all rows that begin with characters and keep only those that begin with numbers in Linux.
hg19 linux
updated 4.4 years ago by 36k • written 4.4 years ago by ▴ 70
0
votes
2
replies
1.6k
views
Variant Calling with Vartrix: Warning with VCF and Error with FASTA
vcf vartrix fasta
4.4 years ago by d • 0
0
votes
0
replies
961
views
DiffBind3 outputs compared to previous versions
DiffBind3 R ChIP-seq EdgeR Deseq2
4.4 years ago by gkunz ▴ 30
134
votes
19
replies
198k
views
13 follow
What'S The Difference Between Cds And Orf?
cds orf
updated 4.4 years ago by • 0 • written 13.3 years ago by ▴ 380
1
vote
0
replies
909
views
Job: Computational Biology Lab Head, Brain Cancer Centre, Melbourne, Australia
cancer wehi australia
4.4 years ago by Gordon Smyth ★ 8.3k
5
votes
4
replies
1.3k
views
BWA-mem alignment
WGS Data Genomics
updated 4.4 years ago by 89k • written 4.4 years ago by ▴ 20
121,895 results • Page 660 of 2438
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Answer: Is a direct comparison of the number of up- and down-regulated genes meaningful?
allele frequency in VCF
Comment: Best way to do protein structure guided similarity search?
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Answer: TCGA -derived Large RangeSummarizeExperient file
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
Answer: Structural Variant identification on pangenome graphs
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Recent Replies
Comment: Pipeline for downloading, aligning, and curating influenza A and B sequences for by GenoMax 153k
Have you looked at https://nextstrain.org/ and specifically https://github.com/nextstrain/seasonal-flu Software is available to do the ana…
Comment: Different UMAP for batch correction in R and Pytho by GenoMax 153k
Use this tutorial for how to upload images: https://www.biostars.org/p/309884/#346553 Only difference is instead of using an external imag…
Answer: GTEx sQTL v8 – annotation version used? by GenoMax 153k
If you click over to the `Reference` tab ( https://gtexportal.org/home/downloads/adult-gtex/reference ), it looks like they used GENCODE v.…
Comment: How to Identify Conserved 21-mers Across TE Insertions in Drosophila? by manikin_python9f ▴ 20
Since they are transposons, we don’t know the exact location of them. We know their sequence of insertions from repeatmasker in dm6 genome.…
Comment: Tool 'sra_source' does not exist. by Atefeh • 0
Thanks for your kindness.
Comment: TCGA -derived Large RangeSummarizeExperient file by Tom • 0
It works well. Thank you very much ! @atpoint
Answer: TCGA -derived Large RangeSummarizeExperient file by ATpoint 89k
For the end user these `DFrames` are just regular data.frames, so you can do `col_data[,c("barcode", "patient", "whatever")]` or just do `a…
Comment: magpurify errors by shevch2009 ▴ 20
I have checked with my eyes, and I didn't find it, I have only one contig that starts with k127_458 .... but the name is different - k127_4…
Comment: Yeast reference-based genome assembly by Michael 56k
So, you aren't sure about the exact species? Then you might want to be careful with reference-based assembly in general. I recommend the fo…
Comment: Structural Variant identification on pangenome graphs by Panos ★ 1.8k
That's a very comprehensive list! Thanks for sharing! `minigraph` better suits my needs because all I need is SVs for my genomes. As far a…
Comment: Yeast reference-based genome assembly by amy967107 • 0
I have ~2.01 Gb of ONT data and the target genome is ~20–23 Mb (90–100× coverage). My ONT read N50 is ~3.8 kb, so contiguity may be limited…
Comment: Yeast reference-based genome assembly by amy967107 • 0
This is a yeast strain (probably Rhodotorula spp.) and I'm trying to assemble the entire genome from nanopore reads using a reference-based…
Answer: Yeast reference-based genome assembly by Michael 56k
The new [hifiassm ONT][1] may be all you need for getting a good assembly. I would not recommend LRSDAY, except for its annotation part (wh…
Comment: magpurify errors by Mensur Dlakic ★ 30k
By the way, these errors are not unique. If you look through the `magpurify` GitHub issues, both types have been reported already. - https…
Comment: magpurify errors by Mensur Dlakic ★ 30k
There is absolutely no chance that a contig labeled `k127_4584534` doesn't exist in your fasta files. These names are not made up out of th…
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