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121,832 results • Page 609 of 2437
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1
vote
5
replies
1.6k
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Filter unique values over columns from a dataframe in R
gene R
updated 4.1 years ago by 21k • written 4.1 years ago by ▴ 10
14
votes
18
replies
8.7k
views
Python script to calculate properties of amino acids
python
updated 2.7 years ago by 45k • written 4.1 years ago by ▴ 140
6
votes
4
replies
2.9k
views
How can read-count from BAM file be greater than than from fastq file?
rna-seq
updated 4.1 years ago by 22k • written 4.1 years ago by ▴ 530
2
votes
3
replies
1.3k
views
Generate consensus from a BAM file to each of the variants
bam coinfection consensus ivar
4.1 years ago by fhsantanna ▴ 620
4
votes
4
replies
2.4k
views
RNA variant calling, aligned with HiSat2
hisat2 gatk splitncigar
4.1 years ago by OhHiImNewHere ▴ 10
1
vote
2
replies
1.2k
views
How to pick top 50 the most abundant pathways?
pathways abundant
4.1 years ago by arshad1292 ▴ 110
1
vote
1
reply
1.1k
views
News: Online Course - A Practical Introduction to NGS Data Analysis (September 15-17, 2021)
workshop DNAseq RNAseq
updated 4.1 years ago by ▴ 590 • written 4.1 years ago by 11k
2
votes
3
replies
1.7k
views
snakemake error: MissingInputException
pipeline snakemake
updated 4.1 years ago by ▴ 580 • written 4.1 years ago by • 0
0
votes
1
reply
835
views
Adding fakes genotypes columns to a vcf file
bcftools vcftools vcf genotype
updated 4.1 years ago by ▴ 480 • written 4.1 years ago by • 0
0
votes
0
replies
647
views
metagenemark model file
metagenemark metagenome prokaryote
4.1 years ago by bioinfo_ga ▴ 70
5
votes
6
replies
2.1k
views
Any Tools to calculate specific gene coverage from BAM file?
Coverage
4.1 years ago by koay • 0
45
votes
2
replies
39k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa
updated 2.6 years ago by 45k • written 13.4 years ago by ▴ 540
0
votes
1
reply
972
views
Association analysis with SNP
association WGS GWAS SNP WES
updated 4.1 years ago by ▴ 1000 • written 4.1 years ago by ▴ 40
1
vote
2
replies
1.3k
views
Batch verify hairpin structure
miRNA
4.1 years ago by 153348734 • 0
1
vote
1
reply
1.8k
views
ChEMBL ID to Ensembl ID
ChEMBL Ensembl
updated 4.1 years ago by ★ 1.1k • written 4.1 years ago by ★ 9.6k
9
votes
10
replies
2.8k
views
How to use Poisson distribution to get meaningful expression counts?
statistics rna-seq
updated 4.1 years ago by 22k • written 4.1 years ago by ▴ 530
3
votes
2
replies
1.1k
views
Add text to fasta header based in a list
fasta header R bash
updated 4.1 years ago by 21k • written 4.1 years ago by ▴ 30
1
vote
2
replies
1.6k
views
snpEff ERROR_CHROMOSOME_NOT_FOUND GRCh37.75 genome
annotaion vcf genomics variant snpEff
4.1 years ago by rbioinfo ▴ 40
1
vote
5
replies
1.7k
views
HaplotypeCaller doesn't output the VCF
BAM VCF GATK HaplotypeCaller
updated 4.1 years ago by • 0 • written 4.2 years ago by ▴ 10
0
votes
3
replies
2.2k
views
conversion of case_ids to file_ids TCGA data
TCGA case_ids conversion
updated 4.1 years ago by • 0 • written 6.3 years ago by ▴ 530
1
vote
0
replies
832
views
Kaplan Meier Plotter and Competing risk model survival analysis
Competing risk anaylsis model Kaplan-Meier
4.1 years ago by aronno.geb ▴ 10
0
votes
0
replies
1.2k
views
Stringtie error : discarding overlapping duplicate miRNA feature
miRNA stringtie
updated 14 months ago by 45k • written 4.1 years ago by ▴ 30
0
votes
0
replies
519
views
Germline calling with differents sample source
WGS alignment genome
4.1 years ago by quentin54520 ▴ 120
7
votes
3
replies
2.8k
views
snakemake to merge bams from multiple samples
snakemake
updated 4.1 years ago by ▴ 580 • written 4.1 years ago by ▴ 260
1
vote
2
replies
1.4k
views
Bioinformatic tool for acinetobacter plasmids
plasmidseeker plasmidfinder plasmid
4.1 years ago by blur ▴ 280
0
votes
2
replies
1.2k
views
From case uuid to specific file uuid
TCGA GDC
4.1 years ago by adebola.1 • 0
1
vote
1
reply
1.7k
views
Fastest way to use pysam view in order to get the reads in different regions
pysam_view samtools pysam bam optimisation
updated 4.1 years ago by ▴ 580 • written 4.1 years ago by ▴ 30
0
votes
2
replies
905
views
RNA without replication 2
RNA-Seq
updated 3.2 years ago by 45k • written 4.1 years ago by ▴ 10
1
vote
8
replies
2.2k
views
RNA without replication
RNA-Seq
updated 3.2 years ago by 45k • written 4.1 years ago by ▴ 10
5
votes
5
replies
3.8k
views
Adapter trimming
Trimmomatic Fastqc Adapter
updated 4.1 years ago by ▴ 460 • written 4.1 years ago by • 0
2
votes
1
reply
843
views
why is important to identify genetic risk variants?
genetic risk variants
updated 4.1 years ago by 89k • written 4.1 years ago by ▴ 10
0
votes
0
replies
580
views
3D protein modeling and Docking studies
modeling 3D- Docking
4.1 years ago by aronno.geb ▴ 10
0
votes
0
replies
508
views
Constraint based modelling, Flux Balance analysis
analysis Flux Balance
4.1 years ago by ShiwangiW • 0
3
votes
2
replies
4.2k
views
Why ATAC-seq/CUT&RUN need paired-end sequencing?
HiC sequencing
updated 4.1 years ago by • 0 • written 6.2 years ago by • 0
1
vote
3
replies
1.8k
views
Using BiomaRt returns to get entrez gene ids returns an error. Why is this happening?
BiomaRt R
4.1 years ago by peter.berry5 ▴ 60
1
vote
6
replies
2.4k
views
mapper.pl gives empty output
miRDeep2 Bowtie mapper.pl
updated 4.1 years ago by ▴ 590 • written 4.1 years ago by ▴ 30
1
vote
4
replies
2.1k
views
Abnormal fastq lines
fastq-file-error SRR-flile mapping-error
updated 4.1 years ago by 153k • written 4.1 years ago by ▴ 110
0
votes
0
replies
732
views
Error : no alignment column
Phylip python Vcf Iqtree
4.1 years ago by Kagisoralph • 0
8
votes
6
replies
2.2k
views
Use bioinformatics tool in iphone 7
megax chimera Android modeler
updated 2.7 years ago by 45k • written 4.1 years ago by ▴ 140
5
votes
3
replies
3.9k
views
How to loop to use trimmomatic for multiple fastq files?
linux trimmomatic
updated 4.1 years ago by ▴ 460 • written 4.1 years ago by ▴ 50
0
votes
2
replies
1.1k
views
NGS QC metrics ( comparison )
QC metrics NGS
4.1 years ago by jovecit478 • 0
2
votes
1
reply
1.5k
views
How do you update plink bim file to remove 'chr' string?
plink
updated 4.1 years ago by 11k • written 4.1 years ago by ▴ 50
1
vote
3
replies
1.6k
views
Troubleshooting Missing_Read_Group and Mismatch_Flag_Mate Errors
Picard BWA
updated 4.1 years ago by 153k • written 4.1 years ago by ▴ 60
0
votes
0
replies
531
views
Fine Mapping Program (FOCUS) Stalling on Chromosome 6
FOCUS mapping fine
updated 4.1 years ago by 45k • written 4.1 years ago by • 0
0
votes
1
reply
1.2k
views
How to conduct a genomic SEM with GxE term and term for G effect on E?
sem gwsem gwas GxE genomic
updated 4.1 years ago by ▴ 940 • written 4.1 years ago by ▴ 10
0
votes
0
replies
654
views
Correct way of calculating Titv ratios for QC
QC titv WES ratio
4.1 years ago by diana.cornejo • 0
2
votes
5
replies
2.5k
views
RNA sequence analyzing data using R after DESeq2 (illumina)
RNA-Seq
updated 3.2 years ago by 45k • written 4.2 years ago by ▴ 10
0
votes
3
replies
4.4k
views
How to calculate R2 from GWAS summary statistics?
GWAS MLM LMM chi-square R2
4.1 years ago by okiedokie1208 ▴ 40
0
votes
3
replies
1.1k
views
Differential expression design considerations
RNA-Seq Limma DE Differential_Expression
4.1 years ago by bioinf.questions • 0
2
votes
1
reply
1.2k
views
Multiple BAM files (ccs) input with Lima (PacBio)
Long-read-sequencing PacBio
updated 17 months ago by 45k • written 4.1 years ago by ▴ 10
121,832 results • Page 609 of 2437
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Comment: Parabricks : Number of GPUs requested (2) is more than number of GPUs (0) in the
Answer: Parabricks : Number of GPUs requested (2) is more than number of GPUs (0) in the
Answer: Split chromosome into smaller fragments to save memory when build xg and gcsa in
C: DiffBind error when calling dba.count
Answer: CBioPortal: What does Mutation type: Targeted_Region means?
Answer: CBioPortal: What does Mutation type: Targeted_Region means?
Comment: how to start
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Comment: vg input and output files by GenoMax 153k
Have you looked at this page: https://github.com/vgteam/vg/wiki/Basic-Operations There is a pipeline illustration on this page that shows …
Comment: Criteria for choosing variants by ATpoint 89k
To me knowledge, ensembl approach means that you run several tools and then run some sort of filtration and classification approach to deci…
Comment: vg input and output files by Pierre Lindenbaum 166k
vg is a toolkit containing different tools. What are you talking about when you want to use 'input' and 'output' files.
Comment: Parabricks : Number of GPUs requested (2) is more than number of GPUs (0) in the by Pierre Lindenbaum 166k
Thanks for the suggestion. I've got `--gres=gpu:2` in my sbatch header (so I imagine it doesn't change much things (?) ). I also suspect a…
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…
Comment: Parabricks : Number of GPUs requested (2) is more than number of GPUs (0) in the by GenoMax 153k
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…
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