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122,201 results • Page 665 of 2445
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2
votes
4
replies
2.9k
views
20,000 Ensembl gene IDs with external gene name in hg19 but not in hg38
ensembl biomart
4.6 years ago by loughrae ▴ 90
0
votes
0
replies
682
views
Determining RNAseq background noise
rna-seq RNAseq RNA-seq rnaseq RNA-SEQ
4.6 years ago by marcos.georgiades.18 ▴ 10
4
votes
8
replies
2.7k
views
Low no_Feature value after using STAR for alignment
RNA-seq alignment STAR
4.5 years ago by yanyanwu ▴ 20
1
vote
3
replies
2.1k
views
ATACseq batch effect coupled with biological effect
batch-effect ATAC-seq
updated 2.5 years ago by 45k • written 4.6 years ago by ▴ 70
0
votes
0
replies
1.2k
views
setReadable error in ClusterProfiler
error setReadable clusterProfiler
4.6 years ago by WF • 0
0
votes
0
replies
707
views
Repeats that affects NIPT results
NIPT NGS
4.6 years ago by khanhlpbao • 0
0
votes
0
replies
889
views
GATK4 MappingQualityReadFilter
GATK4 MappingQualityReadFilter Mutect2
4.6 years ago by jhy ▴ 10
2
votes
2
replies
1.6k
views
Tool to run statistics on a list of genes and output associated conditions/phenotypes that intersect the most?
phenotypes genes
updated 4.6 years ago by ▴ 220 • written 4.6 years ago by ▴ 10
3
votes
0
replies
877
views
Looking for a tool for metadata management
management relational metadata database
4.6 years ago by boaty ▴ 220
4
votes
4
replies
3.1k
views
Filtering out non-bacterial genomes from metagenomic data
metagenomic bacteria
updated 4.6 years ago by ▴ 220 • written 4.6 years ago by • 0
0
votes
0
replies
1.1k
views
Job: Computer Systems Supervisor
LBL IT EMSL NERSC
4.6 years ago by BerkeleyLab ▴ 70
0
votes
6
replies
3.5k
views
Deeptools: computeMatrix can't read file
deeptools
updated 4.0 years ago by 154k • written 4.6 years ago by ▴ 120
1
vote
5
replies
4.7k
views
Problems with installing adegenet
R error software adegenet gene
4.6 years ago by poecile.pal ▴ 50
0
votes
0
replies
1.5k
views
How to parse Hyphy JSON output into treedata?
JSON Datamonkey R-studio treeio PAML
4.6 years ago by Shola • 0
1
vote
0
replies
1.2k
views
Job: Positions at Molecular Diagnostics Labs, UCLA Health
variant clinical scientist curator molecular
4.1 years ago by Cyriac Kandoth 6.1k
0
votes
0
replies
1.6k
views
Job: Exciting Bioinformatics Engineer position at Stanford University
proteomics multiomics metabolomics
updated 2.5 years ago by 45k • written 4.6 years ago by • 0
4
votes
2
replies
1.1k
views
Reads extraction from a .bam file
samtools
4.6 years ago by kaleb.gatto ▴ 10
4
votes
5
replies
1.9k
views
How to calculate combined expression of two genes
R rna-seq
updated 4.6 years ago by ★ 90k • written 4.6 years ago by ▴ 540
0
votes
0
replies
878
views
phyloP conservation score for Saccharomyces cerevisiae S288C (baker's yeast) genome assembly R64 (sacCer3)
phylop conservation yeast saccer3
4.6 years ago by sanjitsbatra • 0
13
votes
6
replies
24k
views
Trimming TruSeq Universal Adapter (Trimmomatic)
fastq trimming RNA-Seq Trimmomatic
updated 4.6 years ago by • 0 • written 8.9 years ago by ▴ 590
2
votes
4
replies
2.1k
views
Converting samtools view <region> output (multiple reads) into single fasta sequence (consensus?)
coordinate dna samtools view consensus
4.6 years ago by a1ultima ▴ 890
0
votes
2
replies
1.1k
views
Statistical test for QQ-plot comparison of GWAS summary statistics
qqplot GWAS p-values
4.6 years ago by f-rasmussen ▴ 10
57
votes
15
replies
137k
views
11 follow
Tutorial: Using R in Conda
R
updated 16 months ago by ▴ 50 • written 5.4 years ago by ▴ 940
0
votes
0
replies
963
views
SvSeq2 for CNVs insertions
WGS Analysis CNV
4.6 years ago by ICfc97 ▴ 20
3
votes
3
replies
1.4k
views
Check a bam file if it was hard clipped?
Hardclipping BAM IGV
updated 4.6 years ago by 154k • written 4.6 years ago by ▴ 10
0
votes
0
replies
842
views
about the batch correction and integration and normalization of scRNA-seq data
normalization scRNA-seq
4.6 years ago by Bogdan ★ 1.4k
0
votes
1
reply
1.1k
views
Genomic Ranges of data from a chromosome
chromosome DNA GenomicRanges
updated 4.6 years ago by 4.2k • written 4.6 years ago by ▴ 50
4
votes
9
replies
13k
views
question about macs2 --broad-cutoff
ChIP-Seq MACS2 macs2 broadpeak broad-cutoff
4.6 years ago by Yu ▴ 140
0
votes
1
reply
1.0k
views
Quantification of a gene that has copies in multiple chromosomes using featureCounts
gene RNAseq featureCounts
updated 4.6 years ago by ★ 2.2k • written 4.6 years ago by ▴ 40
2
votes
1
reply
1.2k
views
cell type grouping
celltypes singlecell
updated 4.6 years ago by ★ 2.2k • written 4.6 years ago by • 0
0
votes
1
reply
1.4k
views
SCRAN-normalization
scRNA Normalization
updated 4.6 years ago by 90k • written 4.6 years ago by ▴ 110
2
votes
8
replies
2.3k
views
Parsing Dates from Multiple Websites
R
updated 4.6 years ago by 21k • written 4.6 years ago by ▴ 940
0
votes
3
replies
1.1k
views
Functional annotation
Annotation
updated 4.6 years ago by 16k • written 4.6 years ago by • 0
1
vote
3
replies
2.1k
views
Stringtie2 no reference transcript found
alignment rna-seq nanopore stringtie samtools
updated 4.6 years ago by 154k • written 4.6 years ago by • 0
6
votes
3
replies
2.5k
views
SNP names Biomart error: Invalid filters(s): snp_filter
R biomaRt rsid snpname
4.6 years ago by PKW ▴ 110
29
votes
14
replies
34k
views
10 follow
Number Of Reads In A Sam File Which Are Assigned To Each Chromosome?
alignment sam
updated 3.0 years ago by 45k • written 14.0 years ago by ★ 4.1k
2
votes
9
replies
4.1k
views
No SINEs, LINEs, LTR and DNA elements detected by RepeatMasker
repeatmasking RepeatMasker repeat
4.3 years ago by Shri hari ▴ 40
0
votes
0
replies
617
views
Normalization of Microarray data for machine learning classification
machinelearning normalization microarray
4.6 years ago by josyulabiotech • 0
4
votes
4
replies
2.2k
views
Files recognized as gzip but not compressed
Linux gzip BAM Ubuntu
4.6 years ago by beaferbl ▴ 10
0
votes
0
replies
664
views
SNP analysis on abi file
abi snp
updated 2.7 years ago by 45k • written 4.6 years ago by • 0
0
votes
1
reply
635
views
Miropeats
miropeats
updated 4.6 years ago by 90k • written 4.6 years ago by • 0
2
votes
3
replies
1.4k
views
Is linked-read sequencing still a thing for genome assembly?
Sequencing Linked-reads
updated 4.6 years ago by 154k • written 4.6 years ago by • 0
3
votes
2
replies
1.1k
views
Protein partners and interactions
Protein database partners molecular interaction
updated 4.6 years ago by 154k • written 4.6 years ago by ▴ 40
3
votes
9
replies
4.0k
views
if you annotate a vcf with snpeff, how do you know if the annotation are referring to the alternate or reference allele?
annotation snpsift snpeff vep
updated 4.6 years ago by 24k • written 4.6 years ago by ▴ 60
2
votes
3
replies
1.9k
views
is it normal to have zero mitochondria genes counts in my 10X data which is from Cellranger 5.0 count?
10X scRNAseq
updated 4.6 years ago by 13k • written 4.6 years ago by ▴ 60
0
votes
5
replies
2.1k
views
Extract reads counts with featureCounts
RNAseq BAM subread featureCounts
updated 4.6 years ago by 154k • written 4.6 years ago by • 0
1
vote
8
replies
5.2k
views
Haploview formats
Haplotype Analysis
updated 4.5 years ago by ★ 90k • written 4.6 years ago by ▴ 10
1
vote
4
replies
2.7k
views
ShapeIT check problematic SNPs
genotypes imputev2 shapeit problematic
4.6 years ago by SHN ▴ 40
0
votes
0
replies
658
views
Tool to find long gapped k-mers (k ~ 1000)
k-mers gapped motif
4.6 years ago by giova34 ▴ 10
1
vote
1
reply
691
views
RMSD clustering
Clustering
updated 4.6 years ago by ★ 30k • written 4.6 years ago by • 0
122,201 results • Page 665 of 2445
Recent Votes
strong appearing variant not found by haplotypecaller in -ERC mode and deepvariant but with haplotypecaller in normal mode
Answer: How can I easily remove overlapping transcripts, keeping only longest transcript
Answer: Log2 transformation is well used, but is there a good paper that can be used as
Answer: Flatten a GTF
Answer: RNA-seq - Creating SAF from NCBI gff for Subread featureCounts - keep 'gene' or
Can EdgeR of DeSeq be used for Single-cell RNA-seq?
Answer: Getting the overlap between two GTF files
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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!
Comment: ID unifiying across different datasets by GenoMax 154k
In this case the entry notes that this is likely the product of a pseudogene: https://www.uniprot.org/uniprotkb/Q5VTE0/entry and existence …
Comment: Comparison of different RNAseq data sets by DrSmad ▴ 10
Each lab contributes both control and LPS. Example, for cell line A_lab1 did and analysis on control and LPS-6h. Cell line B_lab2 did contr…
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