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10
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13
replies
3.8k
views
How to merge 20K single-sample VCFs *without* using plink or plink2?
genotyping vcf
updated 3.2 years ago by 11k • written 3.2 years ago by ▴ 70
9
votes
3
replies
1.0k
views
How do I extract a fasta sequence using the specific keyword (**Psychro**) ?
protein gene genome
written 3.2 years ago by ▴ 1000
0
votes
4
replies
1.3k
views
NRPS annotation
genome mining
3.2 years ago by Rima ▴ 20
3
votes
4
replies
1.5k
views
Add columns to a file based on matched column and maintain the order of lines using awk
shell awk bash
updated 3.2 years ago by 166k • written 3.2 years ago by ▴ 80
0
votes
0
replies
726
views
__too_low_aQual on htseq-count
rna-seq htseq-count
3.2 years ago by onca ▴ 10
0
votes
0
replies
1.5k
views
I can't do RMSD of two ligands using pymol
pymol
3.2 years ago by Welington ▴ 10
5
votes
3
replies
1.7k
views
Mapping chromosome location to gene ID
bedtools eclip ensembl bed R
updated 2.5 years ago by 45k • written 3.2 years ago by ▴ 30
1
vote
6
replies
2.1k
views
How to convert a VCF 4.1 file to Bam file please?
vcf bam
3.2 years ago by Switch ▴ 10
1
vote
0
replies
515
views
Dataset of RNA-binding proteins and their target genes
datasets proteins RBP RNA-binding
3.2 years ago by asente ▴ 30
0
votes
0
replies
539
views
Finding Allele Frequencies for Multiple SNPs
SNPs
3.2 years ago by gtasource ▴ 60
14
votes
13
replies
10k
views
7 follow
Question about ROH analysis by Plink 1.9
snp next-gen plink
updated 3.2 years ago by ▴ 210 • written 5.8 years ago by ▴ 50
2
votes
2
replies
871
views
Rearranging data frame based on column values
python biopython
updated 3.2 years ago by 45k • written 3.2 years ago by ▴ 60
0
votes
1
reply
738
views
understanding similarity in different sra files
profile expression rna-seq
updated 3.2 years ago by 15k • written 3.2 years ago by ▴ 60
7
votes
7
replies
2.3k
views
How to obtain 200 bp flanking sequence from both sides of BLAST search?
sequence blast genome nucleotide
updated 3.2 years ago by 15k • written 3.2 years ago by ▴ 270
0
votes
0
replies
1.1k
views
Error in createArrowFiles ArchR Analysis
snatac-seq archr scatac-seq archrgenome atac-seq
3.2 years ago by bioinformatics.girl ▴ 30
0
votes
1
reply
1.2k
views
Combining RNA and ATAC
Seurat atac single-cell signac rna
updated 3.2 years ago by ▴ 30 • written 3.2 years ago by ▴ 160
4
votes
2
replies
1.0k
views
Is there any way to normalize a sample with high number of reads assigned to it?
fastp sequencing depth RSEM STAR
updated 3.2 years ago by 21k • written 3.2 years ago by ▴ 70
0
votes
0
replies
924
views
Inserting Junctions Into Genome after Indexing with STAR
splicing alternative Junctions STAR RNA-Seq
3.2 years ago by hkarakurt ▴ 200
2
votes
3
replies
2.5k
views
Reporting results from fastp Read GC content
fastp MultiQC PE sequencing GC
3.2 years ago by salman_96 ▴ 70
0
votes
1
reply
770
views
What does different columns for merged gtf file represents?
StringTie GTF merged
updated 3.2 years ago by 4.8k • written 3.2 years ago by • 0
2
votes
8
replies
2.2k
views
Extracting fasta fsequences based on ID headlists
seqkit fasta grep script
updated 3.2 years ago by 15k • written 3.2 years ago by • 0
0
votes
3
replies
1.0k
views
Extract reads for Anaeroplasma species from whole genome sequencing data
PacBio Assembly Mouse WGS
updated 3.2 years ago by 5.1k • written 3.2 years ago by • 0
1
vote
1
reply
1.1k
views
Physical phasing of polyploid SNPs from RNA-seq data
GATK phasing transcriptome haplotype polyploid
updated 3.2 years ago by 7.8k • written 4.2 years ago by ▴ 50
2
votes
5
replies
1.5k
views
comparing fragmented RNA-seq to non-fragmented RNA-seq
voom differential fragmentation normalization limma
updated 3.2 years ago by ★ 8.3k • written 3.2 years ago by ▴ 40
1
vote
1
reply
1.1k
views
Advice on mapping reads to polyploid de-novo assembly
assembly RNA-Seq
updated 3.2 years ago by 7.8k • written 5.6 years ago by ▴ 750
4
votes
8
replies
3.9k
views
Polyploid genome and mapping !!
alignment next-gen
updated 3.2 years ago by 7.8k • written 8.9 years ago by ▴ 170
1
vote
1
reply
2.1k
views
kraken2 paired end reads not processing
metagenomics kraken2
updated 3.2 years ago by 8.7k • written 3.2 years ago by • 0
0
votes
4
replies
1.2k
views
Comparing bed files for shifts and enlargements
bed bedtools chip-seq
3.2 years ago by Deniz • 0
3
votes
14
replies
3.7k
views
6 follow
Generating thumbnail previews automatically from PDB files
pymol chimera image PDB
updated 3.2 years ago by ▴ 380 • written 3.3 years ago by 56k
0
votes
0
replies
546
views
Minimal insert size for Illumina MiniSeq
insert-size MiniSeq amplicon Illumina
updated 3.2 years ago by 45k • written 3.2 years ago by ▴ 20
0
votes
2
replies
1.9k
views
fastq-dump throws "connection failed" error
SRA fastq fastq-dump
3.2 years ago by shpak.max ▴ 60
0
votes
1
reply
838
views
How do you predict regions on a protein that are exposed on the cell surface?
protein antibody hmm domain
updated 3.2 years ago by ★ 29k • written 3.2 years ago by ▴ 750
0
votes
3
replies
1.1k
views
i got an error message in bowtie2 run
bowtie2_problem
3.2 years ago by carlosgonzalezcruz327 ▴ 20
4
votes
2
replies
1.0k
views
RNA-seq Replicate papers for beginner
alignment R RNA-Seq
3.2 years ago by layan.essam • 0
1
vote
2
replies
1.8k
views
limma voom -- all genes after filtering are differentially expressed
expression differential voom RNAseq limma
updated 3.2 years ago by ★ 8.3k • written 3.2 years ago by ▴ 40
0
votes
0
replies
714
views
Subsetting txdb object by "tx_name"
GRanges R Gviz
3.2 years ago by Trivas ★ 1.9k
2
votes
10
replies
2.2k
views
Linux bash: How to pipe several files?
wildcard pipe Linux
updated 3.2 years ago by 21k • written 3.2 years ago by ▴ 10
4
votes
3
replies
1.4k
views
Create a bed file bins from fasta?
bed fasta
updated 3.2 years ago by 13k • written 3.2 years ago by ▴ 130
0
votes
0
replies
452
views
Giotto: ICGscoresHighGenes: Error in `:=`(spec_int, paste0(cell_type, "--", int_cell_type)) :
Giotto
updated 3.2 years ago by 153k • written 3.2 years ago by ▴ 10
4
votes
2
replies
905
views
Check how many entries in Genbank have a 'rep_origin' feature
annotation feature rep_origin Genbank
3.2 years ago by Zoya • 0
0
votes
1
reply
822
views
VCF files missing some chromosomes info
chromosome VCF infos Missing
updated 3.2 years ago by 103k • written 3.2 years ago by • 0
2
votes
3
replies
1.5k
views
Summarizing transcript level annotation from Trinity de novo assembly to gene level annotation
functional expression differential RNAseq transcriptome enrichment Trinity annotation genes
2.6 years ago by MB ▴ 60
3
votes
4
replies
1.4k
views
Is there a convention or nomenclature for the order of naming base pairs when describing nucleic acid structures and geometry in a publication?
Naming aptamer conventions nomenclature
3.2 years ago by l33thamdog • 0
4
votes
3
replies
1.0k
views
Site where I find dogs gene
Position Gene SNP
3.2 years ago by gosssheen • 0
1
vote
2
replies
1.1k
views
NuGEN Ovation RRBS Methyl-Seq System - How to use nudup.py to remove PCR duplicates- RRBS
PCR_duplicates RRBS NuGEN
3.2 years ago by BB • 0
0
votes
1
reply
771
views
From counts to TPM code verification
TPM normalization r
updated 3.2 years ago by 89k • written 3.2 years ago by ▴ 200
0
votes
1
reply
555
views
Clustering GO
GO clustering
updated 3.2 years ago by 4.8k • written 3.2 years ago by • 0
1
vote
2
replies
1.3k
views
How to identify locus_tag by using RefSeq protein info (WP_*)
NCBI tag RefSeq locus
updated 3.2 years ago by ▴ 800 • written 3.2 years ago by ▴ 30
0
votes
0
replies
563
views
NGS analysis of region with point mutations?
indel point mutations crispr fastq
3.2 years ago by a_bis ▴ 40
0
votes
0
replies
490
views
ERROR: No dogs remaining after --keep in PLINK
PLINK keep GWAS
3.2 years ago by gosssheen • 0
121,832 results • Page 416 of 2437
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Comment: Split chromosome into smaller fragments to save memory when build xg and gcsa in by 李经纬 • 0
Thank you. Even if I build the XG index after some modifications, the building of gcsa failed even on a single chromosome. Even though I h…
Comment: Parabricks : Number of GPUs requested (2) is more than number of GPUs (0) in the by Mensur Dlakic ★ 29k
For posterity, here is `nvidia-smi` output for our cluster: ``` +-------------------------------------------------------------------------…
Answer: Parabricks : Number of GPUs requested (2) is more than number of GPUs (0) in the by Mensur Dlakic ★ 29k
How often do we get a chance to help @yokofakun after all the help Pierre has provided? I feel like we have to make a serious effort here. …
Comment: DiffBind error when calling dba.count by Irene • 0
I am having the same issue with the same situation, so i do not understand what could be the problem...i do not know if you finally figure …
Comment: Parabricks : Number of GPUs requested (2) is more than number of GPUs (0) in the by Pierre Lindenbaum 166k
@genomax I'm using the 'GPU' queue of my cluster (SLURM). The very same config was used with another parabrick subtool and I got not probl…
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Are you running this under a job scheduler? Is there a separate partition for the GPU's/are they accessible to the scheduler?
Comment: Learning Bioinformatics doing Projects by Anjali • 0
thank you.
Comment: Statistical test of difference between two conditions and account for the batch by ATpoint 89k
Are the batches biological replicates?
Comment: how to start by shelkmike ★ 1.7k
If you want to save time at the cost of having a lesser understanding of how bioinformatic programs work, you may study through the BioStar…
Answer: how to start by shelkmike ★ 1.7k
I would recommend, in the following order:<br> 1) Go through Bioinformatics Algorithms, either as a video course or as a book, and do all e…
Comment: Perform Hierarchical Clustering in R with ggdendro Visualization by Bastien Hervé 6.4k
For what is worth, in a previous project, I have done some tests on different hierarchical clustering methods for single cell RNAseq. I had…
Answer: how to start by yura.grabovska ▴ 820
* Get some data - either your own or from a paper / GEO / ArrayExpress / SRA / TCGA / cBioPortal etc etc. * Look at the methods of papers…
Comment: Perform Hierarchical Clustering in R with ggdendro Visualization by ATpoint 89k
"ward.D2" -- top of the pops in terms of interpretatble clusters from gene expression data in my hands, the rest is...often crytpic.
Comment: High percentage of intronic/intergenic reads in RNA-seq by i.sudbery 22k
I'd expect to see more or less what they see in your reference. Somewhere between half and two thirds of reads mapping to exons. The low fr…
Comment: Perform Hierarchical Clustering in R with ggdendro Visualization by Bastien Hervé 6.4k
As the whole presentation relies on a distance matrix and elements aggregation by hierarchical clustering, it would be helpful to better un…
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