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122,202 results • Page 688 of 2445
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805
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Find genomic coordinates for exons in historical transcripts
genome exon human coordinates
4.7 years ago by raptly61549 • 0
0
votes
0
replies
2.6k
views
Troubleshooting abnormal ATAC-seq diagnostic plots
QC Sequencing ATAC-seq Troubleshooting
4.5 years ago by cwwong13 ▴ 40
2
votes
5
replies
3.0k
views
align interleaved fastq file
interleaved fastq align
updated 4.7 years ago by 154k • written 4.7 years ago by ▴ 20
0
votes
0
replies
816
views
Merging Output from Trinity and Go analysis
transcriptome merge assembly
4.7 years ago by dimitrischat ▴ 210
3
votes
3
replies
2.1k
views
Can I pool RNA-seq library with ATAC-seq library and sequence in the same S4 lane?
RNA-seq Sequencing ATAC-seq
updated 4.7 years ago by 154k • written 4.7 years ago by ▴ 40
1
vote
4
replies
2.0k
views
BAM file's reference sequence IDs doesnt match contigs ID's
metagenomics alignment bam
updated 2.7 years ago by 45k • written 4.7 years ago by ▴ 140
1
vote
3
replies
2.7k
views
Nanopore structural variant calling - more than 2 alleles on IGV track?
nanopore structural variant igv vcf
updated 5.6 years ago by • 0 • written 5.9 years ago by ▴ 200
3
votes
2
replies
1.4k
views
sharing a cytoscape installation with multiple terminals
server hpc cytoscape
updated 4.7 years ago by ▴ 310 • written 4.7 years ago by • 0
6
votes
4
replies
2.4k
views
merge .fastq.gz files
RNA-seq
updated 4.7 years ago by 15k • written 4.7 years ago by ▴ 260
4
votes
4
replies
3.4k
views
RNA velocyto scRNA-seq install
gcc about some version questions
updated 4.7 years ago by 13k • written 4.7 years ago by ▴ 90
0
votes
2
replies
1.3k
views
Combining multiple Streak variant files with their filename
NGS VCF Strelka2
4.7 years ago by parvathi.sudha ▴ 40
1
vote
0
replies
1.8k
views
News: Webinar - Recent and upcoming enhancements in web BLAST and Primer-BLAST! (Wed, April 7, 2021 12:00 PM - 12:45 PM EDT)
primer-BLAST blast
4.7 years ago by GenoMax 154k
3
votes
5
replies
2.8k
views
normalize different size fastq files
metagenome data genomics normalization
4.6 years ago by serene.s • 0
1
vote
0
replies
714
views
What the difference between last-split and single2_cov
MSA TBA LAST
4.7 years ago by gengyang12138 ▴ 20
1
vote
1
reply
4.5k
views
Converting VCF from hg19 to hg38
remapping VCF
updated 4.7 years ago by 166k • written 4.7 years ago by ▴ 40
3
votes
2
replies
2.8k
views
bbcms vs bbnorm when working with highly uneven coverage
BBTools Metagenomics Megahit Assembly BBNorm
updated 3.9 years ago by • 0 • written 4.7 years ago by ▴ 170
0
votes
0
replies
781
views
GATK VQSR filter
NA12878 VariantRecallibration
4.7 years ago by esimonova.me ▴ 30
0
votes
0
replies
660
views
Problem in a microbial functional gene analysis.
database Protein
updated 4.7 years ago by 154k • written 4.7 years ago by • 0
0
votes
0
replies
727
views
Why hifi-read SV different from HG002_SVs_Tier1_v0.6.vcf
ccs
4.7 years ago by eioyuou • 0
4
votes
2
replies
2.1k
views
Forum: Why did expression based subtypng of breast cancer gain much more acceptance than others
RNA-Seq subtyping expression
updated 4.7 years ago by 154k • written 4.7 years ago by ▴ 770
0
votes
0
replies
714
views
Tool for pathogen Detection from metagenome
metagenome genomics
updated 2.5 years ago by 45k • written 4.7 years ago by • 0
0
votes
2
replies
3.0k
views
Genes whose names starts with AL
whose AL Genes starts with names
updated 4.7 years ago by 24k • written 4.7 years ago by • 0
1
vote
5
replies
4.9k
views
Miniconda InvalidArchiveError when downloading FastQC
conda fastqc
updated 2.7 years ago by 45k • written 4.7 years ago by ▴ 10
4
votes
2
replies
1.4k
views
Finding genes under positive selection in non-model species - Phylotranscriptomics approach ?
gene ortholog assembly rna-seq
updated 24 months ago by 45k • written 4.7 years ago by ▴ 1000
1
vote
4
replies
2.0k
views
problem with SNPs and Indels detectiong useng WGS data
WGS
updated 4.7 years ago by 45k • written 4.7 years ago by ▴ 280
0
votes
5
replies
2.1k
views
Using Statistical enrichment test for groups Principal Component Analysis
PCA
4.6 years ago by Gabriel ▴ 180
0
votes
4
replies
1.8k
views
How to create an heatmap of clusters obtained by degpatterns function?
R RNAseq degpatterns clusters DESeq2
updated 4.6 years ago by 45k • written 4.7 years ago by • 0
0
votes
0
replies
669
views
How to predict gene promoters in Lactobacillus?
lactobacillus promoters
4.7 years ago by A_heath ▴ 180
1
vote
5
replies
2.2k
views
calculation synonymous and non-synonymous allele counts in a VCF file
VCF
updated 4.7 years ago by 14k • written 4.7 years ago by ▴ 30
1
vote
2
replies
3.0k
views
visualize phased vcf file
vcf phasing
updated 4.7 years ago by ▴ 640 • written 4.7 years ago by ▴ 290
1
vote
1
reply
2.2k
views
BLAT standalone version - why is it so slow?
BLAT
updated 4.7 years ago by 36k • written 4.7 years ago by • 0
0
votes
1
reply
2.7k
views
How to download individual-level genotype data from gnomAD or EXAC
data genotyping genome
updated 4.7 years ago by ▴ 270 • written 4.7 years ago by • 0
0
votes
0
replies
1.1k
views
miRDeep2 Support
miRNA mirDeep2
4.7 years ago by VineethVenumadhavan ▴ 50
2
votes
4
replies
6.7k
views
Visualizing VCF file on IGV
BCFTOOLS VCF IGV
updated 4.7 years ago by 154k • written 4.7 years ago by ★ 2.5k
6
votes
4
replies
4.7k
views
RSEM gene-level estimates to DESeq2
RNA-seq DESeq2 RSEM DGEA
updated 4.7 years ago by 90k • written 4.7 years ago by • 0
2
votes
7
replies
5.4k
views
extract unmapped reads from the paired end samples using hisat2
pairedends hisat2 unmappedreads snakemake
4.7 years ago by winmoon6 • 0
0
votes
0
replies
701
views
How important is aligning BAM files to the appropriate design file?
gatk sequencing genomics wes bam
4.7 years ago by jon.klonowski ▴ 210
1
vote
8
replies
4.9k
views
Conserved markers between clusters (not between stim/exp etc)
Seurat Conserved Markers R
updated 4.7 years ago by • 0 • written 5.3 years ago by • 0
0
votes
6
replies
4.3k
views
Best compression for single cell RNA-seq object
seurat rna-seq scanpy single-cell scRNA-seq
updated 4.3 years ago by • 0 • written 4.7 years ago by ▴ 200
1
vote
2
replies
1.4k
views
Can we add additional columns to ped and map files in PLINK?
PLINK
updated 2.7 years ago by 45k • written 4.7 years ago by • 0
2
votes
1
reply
3.0k
views
clusterProfiler GSEA for upregulated and downregulated gene sets: conflicting results
GSEA clusterProfiler DESeq2
updated 4.7 years ago by ▴ 60 • written 6.0 years ago by ▴ 30
11
votes
5
replies
3.9k
views
NovaSeq Duplicates
duplicationrate ChIP-seq
updated 3.4 years ago by 16k • written 4.7 years ago by ▴ 20
1
vote
4
replies
3.1k
views
How can I download the PCAWG (ICGC/TCGA) raw counts data?
ICGC RNA-Seq PCAWG
4.7 years ago by Sonia • 0
0
votes
1
reply
1.0k
views
How do I determine antibiotic resistant gene from a metagenome
metagenomics genomics antibioticresistantgene
updated 4.7 years ago by ▴ 590 • written 4.7 years ago by ▴ 10
0
votes
1
reply
1.0k
views
Converting REVIGO treemap csv to CirGO format
cirgo revigo
updated 4.7 years ago by 9.0k • written 4.7 years ago by ▴ 10
1
vote
2
replies
1.3k
views
makeblastdb performance benchmark
makeblastdb performance runtime memory blast
4.6 years ago by drquestion ▴ 20
6
votes
3
replies
1.8k
views
Running blastn to get best hits match using (-max_target_seqs 1 -max_hsps 1 ) ?
blast alignment
4.7 years ago by sunnykevin97 ▴ 1000
4
votes
3
replies
2.2k
views
Exporting the list of top loading genes from a particular principal component
PCAtools
updated 4.7 years ago by ★ 90k • written 4.7 years ago by ▴ 80
1
vote
2
replies
2.0k
views
identifying strain using pangolin and nextclade
Covid19 pangolin nextstrain strain nextclade
4.7 years ago by eli_bayat ▴ 100
1
vote
0
replies
925
views
News: SBGNview: Data Analysis, Integration and Visualization of All Pathways
SMPDB PANTHER Reactome SBGNview Pathview
4.7 years ago by bigmawen ▴ 440
122,202 results • Page 688 of 2445
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How to trim transcripts using information from NCBI contamination screen report
How to trim transcripts using information from NCBI contamination screen report
Trimming sequences based on NCBI contamination screen report
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Answer: Chip-seq analysis Diffbind by ATpoint 90k
I think the results are expected. a) n=2 is underpowered, for any assay and in particular for ChIP-seq which has considerable noise. b) you…
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Wu-Sheng Zhang ▴ 10
Hi @arup , after changing the file name following the read length, I can process them using cellranger arc successfully. Thank you very muc…
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 ▴ 10
Got it! I will try to switch their name and re-run the cellranger arc. Thank you very much, @arup !
Answer: 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 ▴ 10
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…
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