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Correct steps to perform a majority consensus phylogeny in RaxML
phylogeny raxml maximum-likelihood bootstrap
4.6 years ago by ddh8602 • 0
24
votes
14
replies
7.4k
views
6 follow
How To Generate Dna K-Mers Of A Given Length In C?
c programming
updated 4.6 years ago by 45k • written 13.7 years ago by ▴ 50
0
votes
0
replies
674
views
should I scale a MASH matrix ?
scale MASH
4.6 years ago by v.berriosfarias ▴ 140
2
votes
1
reply
1.2k
views
Independent Filter returns null value with attr(DESeq2Res, 'filterThreshold')
DESeq2 Filtering
updated 4.6 years ago by 90k • written 4.6 years ago by ▴ 70
0
votes
3
replies
1.5k
views
Transcript enrichment in Illumina RNAseq
enrichment transcriptomics illumina rnaseq
4.6 years ago by compuTE ▴ 140
0
votes
2
replies
978
views
Help with MrBayes parameters
Mrbayes
updated 4.6 years ago by ★ 30k • written 4.6 years ago by • 0
28
votes
2
replies
7.8k
views
Tutorial: Extracting genomic feature sequences from GTF/GFF files with AGAT
extract GTF GFF sequence
updated 3.2 years ago by ▴ 40 • written 4.6 years ago by 9.3k
4
votes
4
replies
4.9k
views
Understanding the ColData Matrix
RNA-SEQ R Micheal_Love DESEQ2
updated 4.6 years ago by 9.0k • written 4.6 years ago by ▴ 30
13
votes
14
replies
10.0k
views
9 follow
Tool: open-cravat: variant annotation tool
open-cravat
updated 2.5 years ago by 45k • written 7.0 years ago by ▴ 260
2
votes
7
replies
6.6k
views
Samtools view error:
bowtie Samtools
updated 2.7 years ago by 45k • written 5.1 years ago by ▴ 110
1
vote
1
reply
3.6k
views
sam_hrecs_error Malformed key:value pair
alignment
updated 4.6 years ago by 154k • written 5.8 years ago by ▴ 440
1
vote
1
reply
1.7k
views
Reactome website gene expression analysis
gene_expression_analysis_tool Reactome_website
updated 4.6 years ago by 154k • written 4.6 years ago by ▴ 160
0
votes
2
replies
1.4k
views
NanoString output: miRNA probe ID with with plus sign (+)
nanostring mirna
4.6 years ago by kinnaryshahh • 0
6
votes
10
replies
3.9k
views
Pacbio SRA data format error
Pacbio SRA bax2bam isoseq3
updated 4.6 years ago by ▴ 40 • written 4.8 years ago by ▴ 20
0
votes
0
replies
1.1k
views
Error while using pybiomart package
biomart pybiomart
4.6 years ago by ahmedmelmoselhy ▴ 20
0
votes
0
replies
828
views
Map LINCS perturbagen identifiers to ChEMBL identifiers?
LINCS L1000 ChEMBL
4.6 years ago by n.y.bell • 0
0
votes
0
replies
1.1k
views
Bowtie2 error: skipping reads
kneaddata bowtie02
4.6 years ago by pdhrati02 ▴ 30
7
votes
4
replies
2.1k
views
very short 'time series' bulk rna-seq, testing two conditions
rna data
updated 4.6 years ago by 90k • written 4.7 years ago by ▴ 10
6
votes
8
replies
2.2k
views
Joining blast hits together into single fasta sequence
sequence genomics blast
updated 4.6 years ago by 21k • written 4.6 years ago by ▴ 70
0
votes
0
replies
915
views
D Prime GWAS
Linkage GWAS
4.6 years ago by Filago ▴ 110
0
votes
0
replies
714
views
Metabolite identification from m/z and retention time
metabolomics R
4.6 years ago by mm2568 • 0
0
votes
0
replies
1.0k
views
TPM biological replicates, geometric mean
TPM tsi tissue
4.6 years ago by joha ▴ 10
19
votes
9
replies
3.5k
views
8 follow
Forum: Future of Microarrays
Microarrays
updated 4.6 years ago by 22k • written 4.6 years ago by ▴ 20
3
votes
2
replies
1.3k
views
Key and value parse with regex
python regex
updated 4.6 years ago by 13k • written 4.6 years ago by ▴ 40
0
votes
2
replies
1.4k
views
How to use DownsampleSam quickly and efficiently with multiple PROBABILITies?
picard downsampling RNA-seq BAM
4.6 years ago by -IvanWoo- • 0
0
votes
0
replies
1.1k
views
differential gene expression (DGE) using TCGABiolinks
DGE TCGA tcgabiolinks
4.6 years ago by peter ▴ 20
2
votes
6
replies
2.6k
views
RRBS ANNOTATION
NGS ANNOTATION RRBS
4.6 years ago by GiV17 ▴ 50
0
votes
4
replies
1.7k
views
Gatk bam metrics
ngs metrics Gatk bam
updated 3.7 years ago by 45k • written 4.6 years ago by ▴ 30
1
vote
1
reply
1.7k
views
split vcf file into multiple files
WGS vcf bcftools
updated 4.6 years ago by 166k • written 4.6 years ago by ▴ 10
3
votes
8
replies
2.8k
views
Convertion Of Gff3 To Gtf
gtf gff
4.6 years ago by daalsa98 ▴ 10
59
votes
23
replies
55k
views
14 follow
Bam File: Change Chromosome Notation
samtools bam
updated 4.5 years ago by 12k • written 14.1 years ago by ▴ 160
3
votes
3
replies
1.3k
views
Phylogenetic tree of gene clusters
evolution clusters phylogeny
updated 4.6 years ago by 22k • written 4.6 years ago by ▴ 180
2
votes
2
replies
9.7k
views
[E::idx_find_and_load] Could not retrieve index file for 'xxxxxsorted.bam'
rna-seq
4.6 years ago by jenyfer ▴ 10
0
votes
2
replies
1.6k
views
NIPT related tools & software
NIPS
4.5 years ago by smrutimayipanda ▴ 20
15
votes
4
replies
8.2k
views
TMM-Normalization
TMM RNAseq-Normalization
updated 7 weeks ago by ▴ 380 • written 4.6 years ago by ▴ 110
0
votes
0
replies
841
views
How to annotate variants against hs37d5?
SNP annotation
4.6 years ago by vinayjrao ▴ 260
1
vote
2
replies
1.3k
views
genomicdbImport issue
genomicdbImport gatk
4.5 years ago by ijlal.hyder2012 ▴ 20
0
votes
3
replies
1.7k
views
Skewed Betweenness Centrality values resulting in almost unusable PPI networks for my university project - what can I do?
Cytoscape
updated 4.4 years ago by 45k • written 4.6 years ago by ▴ 20
0
votes
0
replies
826
views
How to sort and rank compounds docked with AutoDock Vina when the result is presented as only single decimal number?
Docking autodockVina VS VirtualScreening
4.6 years ago by srdjanmasirevic2 ▴ 20
0
votes
1
reply
2.0k
views
RagTag assembly after spades
spades conting ragtag scaffolds
updated 4.6 years ago by ▴ 640 • written 4.6 years ago by ▴ 10
9
votes
4
replies
15k
views
Installing perl modules on a conda environment produce changes out of the environment?
conda perl
updated 4.6 years ago by 8.9k • written 4.6 years ago by ▴ 140
1
vote
0
replies
1.0k
views
Codon alignment with degenerate nucleotides?
paml codeml codon alignment
4.6 years ago by DNAlias ▴ 40
3
votes
1
reply
5.7k
views
add patient information to the metadata or Make New Orig.ident in seurat object
R RNA-SEQ Seurat
4.6 years ago by Maria17 ▴ 40
2
votes
3
replies
1.7k
views
RNAseq
stringtie rnaseq error gffcompare
4.6 years ago by mtavakoli4030 ▴ 10
1
vote
2
replies
2.9k
views
Duplicated Gene Symbol names after geneID conversion
geneID
updated 4.6 years ago by 154k • written 4.6 years ago by ▴ 70
1
vote
1
reply
1.4k
views
How to merge two GTFs which share some common features
stringtie GTF annotation
updated 4.6 years ago by 154k • written 4.6 years ago by ▴ 40
0
votes
0
replies
1.1k
views
my gffcompare out put gtf file is like that. on complete row is followed by some uncomplete row wich have not class codes.
gffcompare rna lncrna gtf
updated 4.6 years ago by 154k • written 4.6 years ago by ▴ 10
1
vote
1
reply
1.2k
views
Performance metrics of aligners and variant callers
benchmarking WGS
updated 4.6 years ago by 23k • written 4.6 years ago by ▴ 10
2
votes
2
replies
1.7k
views
News: Bioinformatics Solutions on AWS
Cloud AWS
updated 4.4 years ago by 45k • written 4.6 years ago by ▴ 20
9
votes
13
replies
3.6k
views
single tumor vs multiple normal sample differential gene expression (RNA-Seq ) analysis using DESeq2
RNA-Seq DESeq2
updated 4.6 years ago by 45k • written 4.6 years ago by ▴ 30
122,202 results • Page 676 of 2445
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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?
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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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