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122,217 results • Page 727 of 2445
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0
votes
7
replies
1.4k
views
Access to public exome files
next-gen
updated 4.8 years ago by 2.9k • written 4.8 years ago by ▴ 30
0
votes
0
replies
1.1k
views
Difference between ATAC fragments and counts files
ATAC-seq Signac
4.8 years ago by i.am.filippov ▴ 10
6
votes
6
replies
2.0k
views
Robustness of Different Normalization Approaches
RNA-Seq DESeq2 edgeR
updated 4.8 years ago by 20 • written 4.8 years ago by ▴ 30
0
votes
0
replies
988
views
News: ONLINE training - Single-cell RNA-seq analysis with R/Bioconductor. 07-11 June
Bioconductor RNA-Seq Single-Cell R
updated 2.8 years ago by 45k • written 4.8 years ago by ★ 2.7k
6
votes
10
replies
2.0k
views
creating virtual library preparation of all possible exons in a gene in human
exons fasta human library preparation
updated 4.8 years ago by 166k • written 4.8 years ago by ▴ 40
0
votes
4
replies
1.9k
views
downsample vcf error
sequencing
updated 4.8 years ago by 166k • written 4.8 years ago by • 0
2
votes
7
replies
1.6k
views
what algorithm can be used to prove that two different diseases have similar genetic signature?
RNA-Seq gene
4.8 years ago by firstorthopedicdoctor ▴ 30
0
votes
0
replies
1.0k
views
WGCNA depencency from GO.db
RNA-Seq
4.8 years ago by acs • 0
2
votes
4
replies
2.8k
views
extracting fastq's from a vcf file
Assembly genome alignment
updated 4.8 years ago by ▴ 640 • written 4.8 years ago by ▴ 50
0
votes
3
replies
2.2k
views
How to retrieve the list of rsid from .bgen file?
snp bgen plink R
updated 4.5 years ago by • 0 • written 4.8 years ago by • 0
0
votes
0
replies
779
views
VCF files unannotated files from The Cancer Genome Atlas
tcga vcf
4.8 years ago by yussab ▴ 100
0
votes
1
reply
1.6k
views
Splitting info field in Annovar's multianno.txt file
Annovar sed awk bcftools
4.8 years ago by a.j.wilson0000 ▴ 10
6
votes
7
replies
1.4k
views
protein multiple alignment
alignment
4.8 years ago by Mohammad Salehi ▴ 30
1
vote
5
replies
1.5k
views
biomaRt external_gene_name same entry multiple times when mapping to homolog mouse gene
ensembl mapping homology
4.8 years ago by nhaus ▴ 420
0
votes
3
replies
1.2k
views
Reorder filter options in PLINK
PLINK QC
4.8 years ago by panacotaforcota • 0
0
votes
2
replies
1.0k
views
get fasta sequences of differentially expressed gene
RNA-Seq cufflinks
updated 4.8 years ago by 154k • written 4.8 years ago by • 0
0
votes
2
replies
1.5k
views
Comparing gene expression in cancer vs. control
RNA-Seq CCLE
updated 4.8 years ago by ★ 90k • written 5.3 years ago by ▴ 100
4
votes
8
replies
3.3k
views
No space left on device error with deeptools bamCompare
software error deeptools picard bash terminal
updated 4.8 years ago by ★ 90k • written 5.4 years ago by • 0
0
votes
1
reply
990
views
GEO2R software 'BART' not working? and is there any good interactive volcano plot library?
R
updated 4.8 years ago by ★ 90k • written 4.8 years ago by ▴ 20
112
votes
56
replies
53k
views
23 follow
Gene Fusion Detection: Rna-Seq Data
rna-seq next-gen sequencing fusion
updated 3.2 years ago by 45k • written 13.5 years ago by ▴ 380
1
vote
4
replies
1.9k
views
NGS/GATK pipeline returns too many variants
NGS WES GATK Mutect
updated 20 months ago by • 0 • written 4.8 years ago by ▴ 190
2
votes
9
replies
5.9k
views
How to remove illumina universal adapter
ChIP-Seq RNA-Seq
updated 4.8 years ago by 154k • written 4.8 years ago by ▴ 20
0
votes
4
replies
2.3k
views
Conversion of GFF3 file to ptt format
RNA-Seq alignment R sequencing next-gen
4.8 years ago by qstefano ▴ 20
0
votes
1
reply
3.1k
views
post-hoc (Tukey) on adonis (permanova)
R statistics
4.8 years ago by mario_de_manner ▴ 20
0
votes
0
replies
805
views
vg de novo calling strategy
vg
4.8 years ago by alexis.simon • 0
0
votes
5
replies
1.7k
views
Analysis of genotype g.vcf
somatic mutations vcf genotype gvcf R Python
4.8 years ago by nikitanaik224 ▴ 20
2
votes
2
replies
1.4k
views
denovo assembly of RNA-Seq data obtained from different platform.
RNA-Seq Assembly batch-effect illumina 454
4.8 years ago by 1234anjalianjali1234 ▴ 60
0
votes
3
replies
3.4k
views
R package for protein-ligand docking
R small molecule docking
updated 4.8 years ago by 27k • written 4.8 years ago by ▴ 30
1
vote
5
replies
2.0k
views
abyss-pe crashes when ran on 650k+ reads
assembly abyss software error
updated 4.8 years ago by 20 • written 6.1 years ago by ▴ 10
1
vote
4
replies
4.2k
views
Split plink files from multiallelic to biallelic
Plink
updated 4.5 years ago by • 0 • written 4.8 years ago by ★ 2.1k
0
votes
5
replies
1.5k
views
development of NGS pipeline for variant calling in lung cancer
cancer NGS pipeline snp next-gen
updated 4.8 years ago by ▴ 30 • written 4.8 years ago by ▴ 40
0
votes
1
reply
1.4k
views
How to calculate dN/dS for all ortholog group ?
slac dN-dS Hyphy fel
updated 2.7 years ago by 45k • written 4.8 years ago by • 0
1
vote
2
replies
1.3k
views
Proper script to automate WGS analysis, typically bcftools
WGS bcftools linux automation
4.8 years ago by FL512 ▴ 20
2
votes
2
replies
1.1k
views
What test can be conducted to check ratio between the groups are significant ?
pvalue statistical test p-value cibersort
4.8 years ago by DareDevil ★ 4.5k
4
votes
4
replies
7.1k
views
How to remove chr from VCF file
VCF
updated 4.8 years ago by ▴ 940 • written 4.8 years ago by ★ 2.1k
0
votes
2
replies
1.2k
views
Identifying reading frame for Ribo-Seq reads
RNA-Seq Ribo-Seq A-site
updated 4.8 years ago by ★ 30k • written 4.8 years ago by ▴ 30
0
votes
2
replies
1.7k
views
Error while exporting GEOdataset ( Error in if (num_colors < 256) { : missing value where TRUE/FALSE needed)
microarray
updated 4.8 years ago by ★ 30k • written 4.8 years ago by ▴ 30
0
votes
0
replies
459
views
Getting Distance Score from ClustalW alignment
alignment
updated 4.8 years ago by 20 • written 4.8 years ago by • 0
0
votes
3
replies
2.0k
views
Analyzing processed RNA-seq data: is this TMM normalized?
rna-seq r
updated 4.8 years ago by ★ 90k • written 4.8 years ago by ▴ 130
0
votes
0
replies
773
views
Forum: How to deal with contamination in bulkseq samples? Looking at correlated genes?
RNA-Seq
updated 2.7 years ago by 45k • written 4.8 years ago by • 0
0
votes
0
replies
353
views
Comparing gene expression data between datasets
RNA-Seq rna-seq next-gen gene
4.8 years ago by kpukacz • 0
3
votes
1
reply
6.5k
views
Vcf file to vcf.gz
VCF
updated 2.7 years ago by 45k • written 4.8 years ago by • 0
2
votes
3
replies
2.4k
views
How many nr file in NCBI nr database
nr database
4.8 years ago by Kash ▴ 110
1
vote
4
replies
1.0k
views
Including 2 factors vs 1 factor in Design Formula for DESeq2
R sequencing
updated 4.8 years ago by 15k • written 4.8 years ago by • 0
1
vote
0
replies
1.7k
views
What format are GTDB-Tk newick trees and how to extract specific node?
metagenomics gtdb database phylogeny
4.8 years ago by O.rka ▴ 750
1
vote
1
reply
869
views
Download all GFF annotations from Ensembl
genome
4.8 years ago by Juke34 9.3k
3
votes
2
replies
1.5k
views
Produce a BED file with genomic coordinates outside a given interval
genome alignment
updated 4.8 years ago by 166k • written 4.8 years ago by • 0
3
votes
9
replies
2.0k
views
Zero small RNA counts on both featureCounts and HTseq
rna-seq alignment sequencing
4.8 years ago by ooluwayiose • 0
0
votes
1
reply
1.1k
views
Unable to run a perl sample file on ubuntu
Perl ncbi
updated 4.8 years ago by 20 • written 5.3 years ago by • 0
0
votes
2
replies
979
views
extract split-read from bam/cram file
bam cram split-read soft clip
4.8 years ago by obaid_lama • 0
122,217 results • Page 727 of 2445
Recent Votes
Comment: circos plot for genomic features
Answer: How to perform GO enrichment in non-model organisms?
Comment: circos plot for genomic features
Answer: How excactly is the Q30 is calculated?
A: PCA in a RNA seq analysis
what cause poly-G from NextSeq
what cause poly-G from NextSeq
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Recent Replies
Comment: Issue while running Kenddata. by GenoMax 154k
Look inside the `*.log` files to see if you can get additional clues (and post them here, if you can't figure out things). Check for lines …
Comment: Question about QC and scrublet by Arup Ghosh 3.5k
You can run Scrublet before filtering cells with high gene counts and compare the doublet score vs `n_counts_genes`.
Answer: How to perform GO enrichment in non-model organisms? by lieven.sterck 16k
In first instance you will as you say need to assign GOterms to your genes. eggNOG-mapper is certainly a valid approach to do this indeed. …
Comment: circos plot for genomic features by Matteo Ungaro ▴ 140
@colindaven thanks a lot! `clinker` also seems to be a nice/effective tool to do so. It happens we stuble across a work where they used `Ci…
Comment: circos plot for genomic features by colindaven 8.1k
Why not use something like Jbrowse2 instead ? https://jbrowse.org/jb2/gallery/ You can load both haplotypes, use minimap2 to create a paf …
Comment: How excactly is the Q30 is calculated? by colindaven 8.1k
This is really a question for your instrument provider. Only MGI application specialists and their bioinformaticians can really answer this…
Answer: How excactly is the Q30 is calculated? by GenoMax 154k
[**Phred quality scores**][1] have been in use since the 1990s and early days of human genome project. They were co-opted in the fastq form…
Comment: best practice for diploid variant calling by Matteo Ungaro ▴ 140
@kevin thanks I was experimenting with the following since I already pursued most of the approaches you mentioned and, in practice, they ar…
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…
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