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121,983 results • Page 641 of 2440
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941
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Package/script for random DNA generation with a pattern!
DNA regex methylation
updated 4.3 years ago by ★ 2.9k • written 4.3 years ago by ★ 1.6k
7
votes
7
replies
14k
views
7 follow
ViennaRNA error: ImportError: No module named _RNA
python viennrna
updated 3.3 years ago by • 0 • written 11.4 years ago by • 0
1
vote
2
replies
1.0k
views
Cytoscape JSON file format and STYLE storage
Cytoscape Styles JSON
updated 2.5 years ago by 45k • written 4.4 years ago by ▴ 60
0
votes
0
replies
836
views
Read group: ID, PU definition and multi-lane (same sample)
multilane group_read RG
4.3 years ago by emma.a ▴ 130
1
vote
1
reply
3.0k
views
ValueError: attempt to get argmax of an empty sequence
mtag python2
updated 4.3 years ago by ★ 2.9k • written 4.3 years ago by ▴ 20
1
vote
0
replies
994
views
calculate LCA with MEGAN UE command line mode for multiple bast files
LCA line MEGAN6 command
4.3 years ago by Mathilde Borg Dahl ▴ 10
2
votes
2
replies
3.9k
views
Reference Genome dna, rm or sm??
unmaksed Reference masked genome
4.3 years ago by SKY ▴ 60
0
votes
0
replies
757
views
Job: PhD position: Computational Epigenetics in cancer cell reprogramming
organization chromatin 3D analyses data image proecessing HiCHIP integrative OligoSTORM
4.3 years ago by alessio.zippo • 0
0
votes
5
replies
1.3k
views
How can I drop the MAPQ info of my sam/bam file?
bam
updated 4.3 years ago by 9.0k • written 4.3 years ago by ▴ 90
0
votes
0
replies
870
views
Job: Senior Bioinformatician (Proteomics, Immunocore, UK)
proteomics UK immunocore
updated 4.3 years ago by 45k • written 4.3 years ago by • 0
5
votes
9
replies
1.9k
views
How can I extract mostly expressed genes from a series matrix?
WGCNA R RNA-seq
4.3 years ago by microorganism_001 ▴ 30
1
vote
3
replies
1.3k
views
Downloading data from 1000Genomes
1000Genomes vcf
updated 4.3 years ago by 12k • written 4.3 years ago by ▴ 20
0
votes
4
replies
1.7k
views
> 90% samples, DP > 10
VCF R DP
updated 4.3 years ago by ▴ 480 • written 4.4 years ago by ▴ 110
6
votes
4
replies
2.7k
views
Genome annotation file GFF3 and GTF same? interchangeable?
GTF GFF3 NGS ANNOTATION
4.3 years ago by SKY ▴ 60
0
votes
3
replies
1.1k
views
Forum: what for masters?
microbio masters
updated 4.3 years ago by ★ 2.9k • written 4.3 years ago by • 0
0
votes
1
reply
824
views
PCA and bar plot in Tripal
tripal plots
updated 4.3 years ago by 12k • written 4.3 years ago by ▴ 120
0
votes
2
replies
1.0k
views
How to convert RNAhybrid output to data frame
RNAhybrid
updated 4.3 years ago by 56k • written 4.4 years ago by • 0
2
votes
2
replies
1.6k
views
Using DAVID Web Service to classify genes into functional groups
DAVID-Web-Service david
4.3 years ago by langziv ▴ 70
0
votes
0
replies
969
views
GATK MUTECT2
gatk mutect2
updated 2.6 years ago by 45k • written 4.3 years ago by • 0
0
votes
1
reply
605
views
how to removed the nucleotides from a fastq file (single-end) in conditional
PAS-seq
updated 4.3 years ago by ★ 2.9k • written 4.3 years ago by ▴ 30
0
votes
3
replies
1.8k
views
Mapping fastq files to reference genome
reference-genome mapping fastq
updated 2.0 years ago by 45k • written 4.3 years ago by ▴ 170
1
vote
4
replies
1.3k
views
Header conflicts in concatenated FASTQ file?
FASTQ RNA-seq concatenate
4.3 years ago by Dunois ★ 2.9k
0
votes
1
reply
843
views
samtools depth vs Rsamtools pileup
Samtools RSamtools Bioconductor R
4.3 years ago by chasem ▴ 50
6
votes
4
replies
2.5k
views
how to removed the first two nucleotides from a fastq file (single-end)
CGAE-seq fastq
updated 4.3 years ago by 21k • written 4.4 years ago by ▴ 30
0
votes
0
replies
801
views
Truncated sam File from Resfinder Database in MGmapper
mapping
4.3 years ago by hafiz.talhamalik ▴ 350
0
votes
1
reply
974
views
Query regarding WGCNA module formation
WGCNA RNA-seq
updated 4.3 years ago by 22k • written 4.3 years ago by ▴ 30
0
votes
3
replies
967
views
function annotation
GO
updated 4.3 years ago by ★ 2.9k • written 4.4 years ago by • 0
0
votes
0
replies
612
views
how to annotate mapping peaks within a defined genomic region？
piRNA genome RNA-seq annotation
4.3 years ago by tianshenbio ▴ 190
1
vote
2
replies
2.1k
views
How to print the header of bed file and the lines that belong to chromosome 2
fastq Bed_files fasta Bash
updated 4.3 years ago by 45k • written 4.4 years ago by ▴ 20
0
votes
1
reply
783
views
Best graph/plot to convey gene expression differences across time?
graph plot Gene Expression R
updated 4.3 years ago by ★ 1.7k • written 4.4 years ago by • 0
3
votes
5
replies
1.9k
views
How to use lapply to extract taxonomic information in my species list?
R
4.3 years ago by DNAngel ▴ 260
0
votes
2
replies
1.2k
views
Forum: Study Materials
learning study materials
4.3 years ago by AHa • 0
1
vote
2
replies
1.2k
views
Duplicate markers
duplicate plink markers
4.2 years ago by Alexandra ▴ 20
0
votes
3
replies
1.5k
views
SOAPaligner- 2bwt-builder segmentation fault
soapaligner c linux
updated 4.3 years ago by 45k • written 4.4 years ago by • 0
0
votes
3
replies
1.9k
views
How to perform GO enrichment for non-model species
non-model-species Gene-Ontology GO-enrichment
4.3 years ago by Kumar ▴ 170
0
votes
0
replies
1.2k
views
What is the file .mums created by mummer ?
Mummer Alignment Mummerplot Genome
updated 4.3 years ago by 45k • written 4.4 years ago by ▴ 30
1
vote
0
replies
877
views
Discussion on binning multiple metagenomes at the same time?
binning metagenomics mags
4.4 years ago by O.rka ▴ 750
6
votes
9
replies
3.4k
views
Preparing Target Data
PGS PRS PRSice
updated 4.4 years ago by ★ 4.8k • written 4.4 years ago by ▴ 20
1
vote
6
replies
1.9k
views
Anyone can help me to interpret this ClonalFrameML output?
Recombination ClonalFrameML Phylogenies
updated 3.7 years ago by 22k • written 4.4 years ago by • 0
0
votes
2
replies
902
views
How to get domain/kingdom name in a table of taxid in R tidyverse?
R
4.3 years ago by DNAngel ▴ 260
2
votes
4
replies
1.6k
views
Rsamtools: get nucleotide of read ID X at position P
rsamtools
4.3 years ago by francois ▴ 90
1
vote
2
replies
1.2k
views
Get by-strand base counts at position from cram file
igv cram count strand details
4.3 years ago by davenomiddlenamecurtis ▴ 20
3
votes
5
replies
1.1k
views
Developing algorithms
Microbial genomics
updated 4.3 years ago by 22k • written 4.4 years ago by • 0
1
vote
1
reply
962
views
How to access specific gene data from the NCBI Gene database with Biopython
Biopython
updated 4.4 years ago by 103k • written 4.4 years ago by • 0
4
votes
3
replies
5.6k
views
kraken2 unclassified output does not work with paired reads?
Kraken2
updated 4.4 years ago by 103k • written 4.4 years ago by ▴ 260
4
votes
3
replies
1.4k
views
What do the samtools column names mean
NGS samtools
updated 4.4 years ago by 45k • written 4.4 years ago by • 0
0
votes
6
replies
2.4k
views
How to identify snps in gene
snp identification
4.3 years ago by Ak ▴ 60
1
vote
1
reply
717
views
Extract co-ordinate for iCLIP data?
sequencing linux RNA
updated 4.4 years ago by 103k • written 4.4 years ago by ▴ 130
2
votes
1
reply
1.8k
views
Preparing data for kinship calculations
PRUNING VCF PLINK2 KING
updated 4.4 years ago by 45k • written 4.4 years ago by ▴ 110
2
votes
3
replies
1.3k
views
plotting stacked bar plot with different number and kinds of variables
stackedbarplot ggplot
4.4 years ago by Curls ▴ 40
121,983 results • Page 641 of 2440
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Is this an appropriate command for estimating contaminatin in a germline WGS sample using GATK?
Answer: Dorado in PowerShell on Windows
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Answer: When to merge RNA-seq files with multiple sequencing lanes
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Answer: Corresponding BAM files by GenoMax 154k
You can get BAM files for 10x single-cell data and they can be found under the `Data Access` tab of the SRA record under the `Original Form…
Comment: GTF file for HIV strain pNL4-3 by Ales ▴ 50
All of the genome assemblies are from the LANL compendiu, match accession with GENBANK (>2,000 complete genome assemblies from the 2021 LAN…
Comment: Hisat2 splice sites extract blank files by Ales ▴ 50
hisat2_extract...py scripts make several assumptions about the input GTF files. For example, they require gene_id field to be present for a…
Comment: GTF file for HIV strain pNL4-3 by GenoMax 154k
> This project started from my personal need to improve spliced alignment Are there plans to submit these annotations to NCBI/EBI? Are yo…
Comment: Hisat2 splice sites extract blank files by Ales ▴ 50
Interestingly, HIV/SIV specifically does have quite an elaborate splicing system which regulates translation. However, only one of the spli…
Answer: Analyzing CRISPR and RNAi genome wide screens by Meisam ▴ 250
I'm late to the party but in case someone has the same question: one practical approach is using **rank-based** methods to meta-analyse you…
Answer: meta data analysis for clustering by Meisam ▴ 250
I'm late to the party but one practical approach is using **rank-based** methods to meta-analyse your screens, which basically bypass the n…
Comment: convert genome file to transcriptome file by Ales ▴ 50
Should be noted that the gtf/gff and genomic.fna files for HIV only contain CDS annotations of the 9 ORFs and not the full transcripts. Onl…
Comment: GTF file for HIV strain pNL4-3 by Ales ▴ 50
just wanted to follow up that to address this specific issue we just released HIV transcriptome annotations of alternative splicing featuri…
Answer: GTF file for HIV strain pNL4-3 by Ales ▴ 50
For anyone stumbling on this. We have recently completed reference-grade annotation for several thousand HIV-1 genomes including the HXB2 (…
Comment: Dorado in PowerShell on Windows by sbissi102 ▴ 10
Yes, I found all the barcodes, but could working on WSL affect the basecalling results?
Answer: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions by DdogBoss ▴ 20
Since I was running in stub-run mode, the solution was to make unique names for the FASTQC process like this: touch ${sample}_${rea…
Answer: GUI commercial software for 10x single cell gene expression analysis by Nicole • 0
Many researchers use the CLC Genomics Workbench and Ingenuity Pathway Analysis. CLC can be used to do secondary analysis for your dataset a…
Comment: Diffbind or DESEQ2 Chipseq data by Irene • 0
For example, in this image, the red area represents the differentially acetylated region returned by DiffBind. The green area is a promoter…
Comment: GUI commercial software for 10x single cell gene expression analysis by GenoMax 154k
Interesting pricing model : https://www.nygen.io/pricing Depending on user needs could be used (or certainly tested) for free. And this is …
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