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122,202 results • Page 673 of 2445
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5
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4.6k
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how to run linux code in python
shell python sh bash linux
4.6 years ago by szp770 ▴ 10
0
votes
0
replies
948
views
Job: Staff Scientist and Postdoc in Bioinformatics and Genomics @UMN
genomics RNA-seq postdoc
updated 2.7 years ago by 45k • written 4.6 years ago by ▴ 20
0
votes
0
replies
768
views
Wheat Input IDs for STRING database
PPI Wheat STRING input_ID
4.6 years ago by drishtee_barua • 0
1
vote
1
reply
1.6k
views
Colour in heatmap labels
labels colour heatmap
updated 4.6 years ago by 11k • written 4.6 years ago by • 0
0
votes
0
replies
706
views
Catalog Database to TF binding site
TFBS
4.6 years ago by Shicheng Guo ★ 9.6k
4
votes
3
replies
3.4k
views
R script does not work in snakemake
Snakemake R
4.6 years ago by lmlukoseviciute ▴ 60
0
votes
4
replies
1.4k
views
identification of catabolic genes in soil metagenome shotgun data
shotgun metagenome
updated 4.6 years ago by 3.9k • written 4.6 years ago by • 0
0
votes
4
replies
3.1k
views
How to compute exact P-values for a small data set for Kendall Correlation Matrix and implement it in the corr plot?
Corr Biostatistics Statistics R
updated 4.6 years ago by 45k • written 4.6 years ago by • 0
2
votes
2
replies
1.4k
views
Custom Database in Kraken2: how are plasmids in same fasta file as bacterial genome handled?
Kraken2 plasmid CustomDB
4.6 years ago by Raphaela ▴ 10
2
votes
4
replies
1.2k
views
How an element is accessed in a python list
Python
updated 4.4 years ago by 45k • written 4.6 years ago by • 0
0
votes
2
replies
1.3k
views
why do the header of bwa mapping sam files show [M::main_mem]
shell bwa genome chip mapping
4.6 years ago by szp770 ▴ 10
0
votes
1
reply
1.1k
views
vcf2maf produces large file after merge
vcf2maf
updated 4.6 years ago by 2.9k • written 4.6 years ago by ▴ 10
1
vote
2
replies
1.6k
views
KEGG orthology of microbiome
microbiome KO
4.6 years ago by mrashad ▴ 80
2
votes
2
replies
1.8k
views
Quick code question in TPM conversion from raw counts RNAseq
RNAseq tpm R
4.6 years ago by v.johnson ▴ 30
1
vote
4
replies
1.9k
views
Coordinates long non-coding RNAs
gtf python bedtools rna-seq hg38
4.6 years ago by luffy ▴ 130
1
vote
2
replies
1.4k
views
Adding new samples to single cell rna-seq analysis
batch scRNA-seq seurat
4.6 years ago by maria2019 ▴ 250
2
votes
1
reply
2.2k
views
Samtools reheader Numerical result out of range
samtools header bam
4.6 years ago by Medhat 9.8k
0
votes
0
replies
823
views
Tajima-Nei Distance estimate with BioPerl
DNA Perl BioPerl Tajima-Nei_Distance
4.6 years ago by mauricio.1313 • 0
1
vote
2
replies
11k
views
how to subset Seurat object by gene names
Seurat scRNA
4.6 years ago by leranwangcs ▴ 150
0
votes
1
reply
1.0k
views
Cluster split, Galaxy Aus
galaxy galaxyaus clustersplit
updated 2.7 years ago by 45k • written 4.6 years ago by • 0
1
vote
4
replies
2.0k
views
Downloading viral database
database Virus NCBI
updated 4.6 years ago by 154k • written 4.6 years ago by • 0
0
votes
5
replies
1.7k
views
6 follow
Exome Sequencing Data?
fastq Exome database
updated 4.6 years ago by ▴ 20 • written 4.6 years ago by • 0
1
vote
2
replies
3.0k
views
SNP coordinates to rsID in .bim file
rsID snp plink plink1.9
updated 4.6 years ago by 36k • written 4.6 years ago by ▴ 70
0
votes
0
replies
793
views
getting residuals from dream
dream limma residuals
4.6 years ago by RNAseqer ▴ 300
2
votes
4
replies
2.8k
views
GATK GenomicsDBImport does not support GVCFs with MNPs
GATK MNPs Mutect2 GenomicsDBImport
4.6 years ago by Rodolfo Adrián • 0
0
votes
3
replies
1.2k
views
Using cBioPortal to assess gene expression data?
cBioPortal
4.6 years ago by a.basitkhan1990 ▴ 60
0
votes
1
reply
951
views
Non-european ancestry in eQTL analysis
gwas eqtl
updated 4.6 years ago by ▴ 170 • written 4.6 years ago by ▴ 90
3
votes
1
reply
1.1k
views
Forum: Interested in benchmarks? Please take our survey!
benchmarking
4.6 years ago by Jeremy Leipzig 23k
0
votes
0
replies
910
views
struggle to plot metagene profile with bed files
plot profile metagene
4.6 years ago by Lila M ★ 1.3k
5
votes
4
replies
2.2k
views
Meaning of the column of sam file
reads position sam
updated 4.6 years ago by 166k • written 4.6 years ago by ▴ 10
1
vote
3
replies
4.9k
views
How to deal with the error for "Per Sequence GC Content" in FastQC tool?
sequencing sequence genome fastqc next-gen
updated 4.6 years ago by 154k • written 5.6 years ago by ▴ 20
1
vote
2
replies
1.2k
views
STAR index issues to the step 4
pipeline snakemake STAR mapping
4.6 years ago by aka ▴ 10
0
votes
1
reply
807
views
Output SNP data after imputation
genomic genomics snps snp imputation
updated 4.6 years ago by 2.9k • written 4.6 years ago by • 0
0
votes
3
replies
3.5k
views
How to change headers of fasta files with the help of another file (nucl_wgs.accession2taxid.gz) containing the desired names (taxID_ accession.vers…
wgs GenBank fasta bash Taxonomy
updated 4.6 years ago by 8.7k • written 4.6 years ago by • 0
13
votes
3
replies
5.9k
views
samtools/bcftools mpileup -B option: to use it or not in order to reduce the occurence of false SNPs discovery?
covid-19 mpileup bcftools snp samtools
4.6 years ago by cg1440 ▴ 60
0
votes
0
replies
991
views
How to add annotation information to a plant genome in the treatment of single-cell ATAC with Signac？
annotation Signac plant
4.6 years ago by qzLi0031 • 0
0
votes
1
reply
770
views
How to call small SVs (<50bp) from single end reads?
SNPs single-end-reads SVs
updated 4.6 years ago by 16k • written 4.6 years ago by • 0
4
votes
2
replies
2.3k
views
fastp results, per base content
fastp quality perbasecontent ubuntu
updated 4.6 years ago by 154k • written 4.6 years ago by ▴ 10
0
votes
1
reply
942
views
Each run generate different result
BSMAP WGBS
updated 4.6 years ago by 16k • written 4.6 years ago by • 0
2
votes
2
replies
1.2k
views
reformat.srun won't work
BBMAP fastq reformat.srun cellranger
updated 4.6 years ago by 154k • written 4.6 years ago by • 0
1
vote
7
replies
4.3k
views
ARS-UCD, UMD and Btau reference SNP map files
Cattle rs position chromosome
3.9 years ago by PKW ▴ 110
0
votes
1
reply
1.9k
views
MAST differential expression with batch information
scrnaseq single-cell MAST seurat batch-effect
updated 4.6 years ago by 90k • written 4.6 years ago by ▴ 10
11
votes
7
replies
3.8k
views
Inconsistency between alignment rates of BWA-mem and bowtie2
Bowtie NGS BWA
updated 4.6 years ago by 103k • written 4.6 years ago by • 0
0
votes
1
reply
1.9k
views
Maxbin2 usage for paired end reads
binning paired-end-reads
updated 4.4 years ago by • 0 • written 4.6 years ago by ▴ 140
8
votes
3
replies
2.5k
views
BioMart servers down again...
ensembl biomart
4.6 years ago by Tai ▴ 10
2
votes
4
replies
1.3k
views
BLAST output
blast
updated 4.6 years ago by 154k • written 4.6 years ago by • 0
2
votes
1
reply
872
views
How to extract this information
gtf r rna seq galaxy
updated 4.6 years ago by 11k • written 4.6 years ago by • 0
17
votes
21
replies
21k
views
7 follow
plotting a dotplot with topGO output
RNA-Seq GO topGO dotplot clusterProfiler
updated 3.8 years ago by ▴ 790 • written 5.1 years ago by ▴ 50
1
vote
8
replies
2.3k
views
weird characters in GATK vcf tables
genomics
updated 4.4 years ago by 45k • written 4.6 years ago by • 0
1
vote
1
reply
1.9k
views
Annotate vcf with AF, gene symbol, functional information
vcf gnomad snpeff dbsnp
updated 4.6 years ago by ▴ 840 • written 4.6 years ago by ▴ 250
122,202 results • Page 673 of 2445
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strong appearing variant not found by haplotypecaller in -ERC mode and deepvariant but with haplotypecaller in normal mode
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Comment: Visualize methylation status in Pacbio Hifi read by cmdcolin ★ 4.4k
(as the JBrowse dev) I'm glad to hear this. if you see any trouble with it feel free to let me know, I have tried to keep up to date with m…
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Wu-Sheng Zhang • 0
Got it! I will try to switch their name and re-run the cellranger arc. Thank you very much, @arup !
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Arup Ghosh 3.5k
The barcode files with 24nt read length W71_LUNGrep2_S6_L001_R3_001.fastq.gz and W71_LUNGrep2_S6_L002_R3_001.fastq.gz should be the R2.
Comment: ID unifiying across different datasets by GenoMax 154k
Each database has their own method of annotation/validation. Depending on resources available there may be a lag between the databases in t…
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Wu-Sheng Zhang • 0
Hi @arup , thank you very much for your suggestions, and here are the results -- they seems correct. May I have your suggestions? Thank you…
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding by samuel.a.odonnell ▴ 640
I don't believe merqury ignores softmasked (lower case) nucleotides so I don't think that is the case. From what it sounds like, during th…
Comment: ID unifiying across different datasets by zizigolu ★ 4.4k
Thanks a lot to be helpful I’m trying to build a complete `UniProtID` to `GeneSymbol` lookup table and I’m running into a wall. I’ve alrea…
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by thomas.heigl.ibk ▴ 20
thanks for the quick reply. i posted the screenshot. gatk-internally, there is still the difference using -ERC or not, priot is getting …
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by thomas.heigl.ibk ▴ 20
here the igv view. showing the histogram for all samples plus the reads for one: ![enter image description here][1] and expanded view of …
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Arup Ghosh 3.5k
Check the read lengths to make sure the files are correct.
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by Pierre Lindenbaum 166k
> Any suggestions or help you could share please, show us an IGV screenshot of the position GATK realign the reads locally, discards read…
Comment: Can i use orthofinder for small protein datasets and not full proteome? by alexandrakortsi • 0
By sequence. Thank you for your response!
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding by xinguok794 ▴ 10
Thank you for your reply! Unfortunately, despite running YAHS with `--no-contig-ec`, the QV value of the resulting FASTA file did not impro…
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!
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