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122,202 results • Page 678 of 2445
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5
votes
6
replies
6.9k
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Extract chromosome 1 - 22 fasta file
fasta
updated 3.4 years ago by ▴ 60 • written 4.6 years ago by ▴ 40
1
vote
2
replies
2.1k
views
GATK GenomicsDBImport for consolidate GVCF
GATK GenomicsDBImport consolidate
4.6 years ago by mscpythonstudy • 0
0
votes
2
replies
958
views
Question about methods monitoring the change from dsDNA/RNA to ssRNA/DNA
RNA DNA chaser Substrate
4.6 years ago by Sophie • 0
1
vote
1
reply
981
views
SHAPEIT2 - ERROR "BAD RECOMBINATION RATE"
shapeit2 phasing
updated 4.6 years ago by 2.9k • written 4.6 years ago by ▴ 130
0
votes
0
replies
821
views
How to download pedigree (SNP's) from cattle
pedigree data snp inference haplotype
4.6 years ago by S. Roa ▴ 10
0
votes
0
replies
990
views
Job: Multiple data scientist positions in computational biomedicine
MachineLearning CompBiology
updated 4.4 years ago by 45k • written 4.6 years ago by ▴ 200
5
votes
5
replies
3.0k
views
GSEA for RNA_seq dataset
DEGs GSEA RNA-seq
updated 24 months ago by 45k • written 4.6 years ago by ▴ 20
4
votes
4
replies
1.8k
views
Hunting invisible characters?
adaptor adapter grep
updated 4.6 years ago by 11k • written 4.6 years ago by ▴ 140
0
votes
0
replies
862
views
Alternative Refence Allele in PLINK2 data files
PLINK2 ALLELE
4.6 years ago by carlstat123 • 0
4
votes
12
replies
4.5k
views
How can I Extract Transposable element from a new genome assembly?
genome transposons assembly annotations
4.6 years ago by jaqx008 ▴ 110
2
votes
1
reply
1.1k
views
differential expression analysis
CRITERIA DEGS THRESOLD
updated 4.6 years ago by ★ 30k • written 4.6 years ago by ▴ 20
32
votes
6
replies
15k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
clustering pam arthritis ComplexHeatmap
updated 2.7 years ago by 45k • written 5.5 years ago by ★ 90k
3
votes
2
replies
1.2k
views
SNP's datasets and pedigreees
SNP data inference haplotype pedigrees base
4.6 years ago by S. Roa ▴ 10
0
votes
4
replies
2.3k
views
Arlequin problem (different loci number among different genotypes)
SNP
4.6 years ago by wangh920 ▴ 10
6
votes
3
replies
5.5k
views
Tool: Clustering of short peptide sequences
peptide phage-display clustering
updated 3.2 years ago by 45k • written 10.2 years ago by ▴ 440
0
votes
14
replies
3.5k
views
File conversion from coordinates to genes
conversion
4.6 years ago by storm1907 ▴ 30
2
votes
1
reply
3.3k
views
Phylobayes, Tracecomp Output Interpretation
updated 4.6 years ago by • 0 • written 11.9 years ago by 11k
0
votes
0
replies
807
views
SECAPR issue
SECAPR reads trimmomatic pipeline alignement
4.6 years ago by Begonia_pavonina ▴ 210
1
vote
1
reply
1.1k
views
bulk RNA-seq contamination, lung ambient RNA
mouse bulkRNAseq contamination RNAseq analysis
updated 4.6 years ago by ★ 19k • written 4.6 years ago by ▴ 10
0
votes
1
reply
835
views
Multiply BED scores by a normalization factor in precise intervals in Granges object.
R
4.6 years ago by massimofaggiani • 0
14
votes
5
replies
8.1k
views
Which Fasta file and GTF file to use in STAR alignment
GTF fasta ENSEMBL STAR
updated 2.7 years ago by 45k • written 4.6 years ago by ▴ 40
0
votes
0
replies
1.3k
views
how to combined peak score or other quantitative indicator when identify TF target gene
ChIP-Seq
4.6 years ago by shangguandong1996 ▴ 30
3
votes
4
replies
4.9k
views
How to set variant FILTER in a VCF file based on overlap with regions in a BED file
annotation bed vcf
4.3 years ago by William ★ 5.4k
8
votes
8
replies
4.2k
views
6 follow
Forum: R - A bioinformatic analysis programming language for NGS
NGS R
updated 4.4 years ago by 45k • written 4.6 years ago by ▴ 520
6
votes
11
replies
3.4k
views
Meaning letters in TCGA sample barcode field
GDC Barcode TCGA
updated 4.6 years ago by 45k • written 4.6 years ago by ▴ 30
1
vote
0
replies
1.0k
views
Methylation frequency + and - strand
methylation Bismark
4.6 years ago by Palgrave ▴ 140
0
votes
0
replies
842
views
Error : Fail to open file file.vcf for normalization with vt
normalization vt vcf
4.6 years ago by Nobody ▴ 30
0
votes
2
replies
1.5k
views
Salmon Script Troubleshooting for RNA Seq Data
NextGenerationSequencing RNAseq Bash Slurm Salmon
updated 4.6 years ago by 90k • written 4.6 years ago by • 0
0
votes
0
replies
637
views
Adjusting for the effect of other variables for DGEA in EdgeR
RNASeq edgeR DGEA
4.6 years ago by emilien.hourquet • 0
1
vote
1
reply
1.4k
views
Normalisation before edgeR for RNA-Seq
rna-seq edgeR
updated 4.6 years ago by 90k • written 4.6 years ago by ▴ 590
0
votes
3
replies
1.8k
views
short length amino acids
short amino acids alignment length
updated 4.6 years ago by 154k • written 4.6 years ago by • 0
0
votes
1
reply
1.2k
views
comparing enriched GO terms between species
RNA-Seq go annotation
updated 4.6 years ago by ▴ 20 • written 5.4 years ago by • 0
2
votes
4
replies
1.7k
views
MASURCA error for multiple entries
masurca
updated 4.6 years ago by ★ 90k • written 4.6 years ago by ▴ 10
6
votes
11
replies
4.2k
views
Download all Bacteria accession list from NCBI
number accession NCBI
4.6 years ago by K.Gee ▴ 40
0
votes
0
replies
760
views
Correlation test based on position sliding window for multiple variables
statistics R corr.test
4.6 years ago by User000 ▴ 750
0
votes
1
reply
1.1k
views
Precision of variant calling (INDELs)
INDELs hap.py
updated 4.6 years ago by ▴ 290 • written 4.6 years ago by ▴ 30
0
votes
0
replies
903
views
How can I slicing to RS4 type in rpy2?
rpy2 slicing rs4 rpy
4.6 years ago by dxodnd • 0
0
votes
0
replies
1.0k
views
Trycycler Assembly_Issue in Flye and MInimap2
Flye minimap2 Trycycler
4.6 years ago by Shiv_2 • 0
1
vote
1
reply
870
views
Combining results tables to plot automatecally
DESeq2
updated 4.6 years ago by 15k • written 4.6 years ago by ▴ 10
2
votes
2
replies
3.0k
views
scRNASeq equal number of cells across conditions
scRNAseq seurat
updated 4.6 years ago by 90k • written 4.6 years ago by ★ 4.8k
0
votes
0
replies
868
views
Job: HIRING: Postdoctoral Scholar in Genomic Epidemiology
postdoc epidemiology genomics
updated 4.4 years ago by 45k • written 4.6 years ago by ▴ 30
0
votes
0
replies
1.0k
views
How to filter and impute missing snps in vcf file
Imputation SNPs PLINK VCF
4.6 years ago by Kumar ▴ 170
2
votes
2
replies
1.8k
views
Arlequin
phylogeny
updated 4.4 years ago by 45k • written 4.6 years ago by • 0
5
votes
6
replies
2.3k
views
How to verify putative miRNA
BLAST miRNA putative Automate
updated 4.2 years ago by ▴ 40 • written 4.6 years ago by ▴ 10
0
votes
0
replies
732
views
low unique mapped reads from STAR
sequencing rnaseq Alignment star
updated 4.6 years ago by 154k • written 4.6 years ago by • 0
6
votes
3
replies
2.2k
views
comprehensive bacterial phylogenetic tree with edge lengths for all of RefSeq or Genbank at NCBI?
refseq ncbi tree phylogeny
4.6 years ago by cmo ▴ 90
2
votes
1
reply
1.1k
views
Checking for(a ton of) overrepresented sequences origins from 16S sequencing
Overrepresented Amplicon Blast FastQC Illumina
updated 4.6 years ago by 154k • written 4.6 years ago by ▴ 20
1
vote
2
replies
1.6k
views
multiqc report, should I care for "Per Base Sequence Content" module if using metagenomic datasets?
fastqc multiqc
updated 4.6 years ago by 45k • written 4.6 years ago by ▴ 140
0
votes
1
reply
892
views
RNA seq experiment design - two in house cell lines, data analysis with CCLE
RNAseq batch-effect experiment-design
updated 19 months ago by 45k • written 4.6 years ago by • 0
1
vote
4
replies
2.2k
views
Extract unmapped reads as pairs from (S/B)AM and create corresponding split read files.
bam sam unmapped paired fastq
updated 4.6 years ago by 154k • written 4.6 years ago by ▴ 40
122,202 results • Page 678 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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Answer: Log2 transformation is well used, but is there a good paper that can be used as
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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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