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how to tell the OR or BETA in the OR.or.BETA column in GWAS summary statistics from GWAS catalog?
gwassummary gwascatalog
4.4 years ago by zhoufeng2ye ▴ 10
0
votes
3
replies
1.6k
views
Multiple motif [available in .txt file ] search from large fasta file to find motif frequency then print fasta sequences
motif fasta frequency
4.4 years ago by Swarna Kanchan ▴ 10
2
votes
2
replies
1.3k
views
how to have aligned region in fasta format using blastn?
blastn fasta
updated 4.3 years ago by 45k • written 4.4 years ago by ▴ 80
0
votes
4
replies
2.4k
views
Help with salmon quantification of samples with de novo transcriptome
salmon denovo tximport
updated 4.4 years ago by ▴ 590 • written 4.5 years ago by • 0
2
votes
0
replies
961
views
what are the parameters we should change when we run VariantsToTable of GATK in splitting multi allelic mode?
variantstotable gatk vcf picard
4.4 years ago by DareDevil ★ 4.4k
0
votes
0
replies
416
views
fetching first column as a class attribute in arulesCBA
arulesCBA R
4.4 years ago by hebasamysaeid1 • 0
1
vote
4
replies
2.2k
views
MA plots with similar distribution but display difference in significantly expressed genes
reads MAplot DEG rna DESeq2
updated 4.4 years ago by 11k • written 4.4 years ago by ▴ 10
1
vote
1
reply
1.3k
views
PCA plot making
VCF PCA vcftools SNP
updated 4.4 years ago by ▴ 720 • written 4.4 years ago by • 0
1
vote
0
replies
1.1k
views
Could it be risky to analyse cells that are negative after cell hashing on single cell RNA sequencing?
RNA-Seq singlecell R Seurat
4.4 years ago by charlesgwellem ▴ 10
0
votes
0
replies
993
views
CNVkit flat reference file creation
CNV ces Flatreference CNVkit wes
4.4 years ago by enes ▴ 40
10
votes
4
replies
9.0k
views
What is gnomAD allele frequency
AF gnomAD
updated 20 months ago by ▴ 760 • written 4.5 years ago by ▴ 70
2
votes
3
replies
2.1k
views
Remove reads from bam file that partially covers a region
indel filter bam
4.4 years ago by arbarharw • 0
0
votes
3
replies
1.1k
views
Trim alignment from .sam file based on a specific tab-delimiter .bed file
sam
updated 4.4 years ago by 166k • written 4.5 years ago by • 0
0
votes
0
replies
732
views
SNP Mapping/Characterisation and Patches
GRCh38 prioritisation patches SNP
4.5 years ago by KBMP • 0
0
votes
2
replies
1.2k
views
Help with statistic model
online education R
updated 4.5 years ago by 89k • written 4.5 years ago by • 0
1
vote
2
replies
2.4k
views
Convert multiple rows value retrieved from ensemble biomart to comma separated list for a common ensemble gene ID.
ensembl Biomart R geneontology
updated 4.2 years ago by 45k • written 4.5 years ago by • 0
0
votes
0
replies
949
views
UCSC parameters for converting between human genome builds
genomics bed ucsc genotyping
4.5 years ago by jon.klonowski ▴ 210
5
votes
3
replies
1.8k
views
RNA-SEQ count data as input for Machine Learning
machine learning rnaseq normalize
updated 4.5 years ago by ★ 2.9k • written 4.5 years ago by • 0
2
votes
5
replies
1.9k
views
Extracting only tumor samples from Single cell RNASeq
tumor cell singel RNA
updated 4.4 years ago by ★ 19k • written 4.5 years ago by ▴ 500
9
votes
6
replies
2.1k
views
6 follow
What are some areas where machine learning is applicable in biology and cancer?
software deep learning
updated 4.4 years ago by ▴ 30 • written 5.7 years ago by • 0
6
votes
11
replies
2.8k
views
How are transcriptome annotations published?
RNAseq annotation publish transcriptome
4.1 years ago by Dunois ★ 2.9k
0
votes
2
replies
1.0k
views
Hetero-dimerization analysis with two FASTA files
sequence FASTA python awk bash
updated 4.4 years ago by 45k • written 4.5 years ago by ▴ 320
3
votes
4
replies
1.9k
views
Convert per base bedgraph to Bed format
Bedgraph perbase Bed Bedtools
updated 4.5 years ago by 36k • written 4.5 years ago by ▴ 20
5
votes
4
replies
12k
views
Why is `send` lower than `sstart` from blast format 6 output?
blast genomics
updated 4.5 years ago by • 0 • written 5.6 years ago by ▴ 750
0
votes
0
replies
1.2k
views
bcftools isec not producing sites.txt
bcftools
4.5 years ago by steve ★ 3.5k
3
votes
3
replies
9.3k
views
Single Cell Experiment object to Seurat without losing rowData / colData
scrna-seq seurat sce
updated 4.4 years ago by ★ 19k • written 4.5 years ago by ▴ 590
0
votes
0
replies
764
views
Samtools vcf file filtering
samtools RNAseq sequencing
4.5 years ago by bandanaschapagain ▴ 40
0
votes
2
replies
1.1k
views
integrate two single cell datasets and use transfer learning approach using annotated cell atlas
machine-learning scRNA-Seq
updated 22 months ago by 45k • written 4.5 years ago by ▴ 30
0
votes
0
replies
581
views
[Errno 2] No such file or directory: '0-rawreads' when I run Falcon unzip with hifi data
HiFi Falcon-unzip
4.5 years ago by Feng • 0
1
vote
4
replies
2.2k
views
exon.bed file for coverage
NGS bed coverage bedtools
updated 2.5 years ago by 45k • written 4.5 years ago by ▴ 30
2
votes
21
replies
4.4k
views
How to loop on two fasta files for hetero-dimerization analysis
fasta script python sequence
updated 4.5 years ago by 21k • written 4.5 years ago by ▴ 320
0
votes
2
replies
1.3k
views
Suggestion for modelling transcriptomics analysis
rnaseq wgcna linearmodel deseq2
updated 4.3 years ago by 45k • written 4.5 years ago by ▴ 190
2
votes
7
replies
3.2k
views
Coverage NGS reads
NGS samtools coverage
4.5 years ago by Sabeen ▴ 30
4
votes
7
replies
3.2k
views
How are BWA/bowtie/etc indices built for multiple fasta entries?
index fasta mapping BWA bowtie
4.4 years ago by maxrwjones ▴ 60
0
votes
1
reply
1.7k
views
Create a phenotype file in PLINK format
gwas phenotype plink
updated 4.5 years ago by ★ 4.8k • written 4.5 years ago by ▴ 10
1
vote
1
reply
1.6k
views
BUSCO score goes down after adding 30% more data
racon BUSCO genome canu pilon
updated 4.5 years ago by ▴ 140 • written 4.5 years ago by ▴ 120
5
votes
7
replies
2.9k
views
Data normalization
normalization RNA-seq
4.5 years ago by nolwenn ▴ 10
0
votes
0
replies
787
views
Multiple Sequence Alignment using HMM
MSA HMM
updated 4.2 years ago by 45k • written 4.5 years ago by ▴ 140
0
votes
1
reply
3.4k
views
Seurat obj conversion to Anndata not accurately creating var in a h5ad file
RNA-Seq R Seurat Anndata
4.3 years ago by akh22 ▴ 120
4
votes
4
replies
1.9k
views
Where to get consensus sequences of human transposable elements
database transposons reference
updated 4.4 years ago by 5.3k • written 4.5 years ago by 48k
2
votes
13
replies
3.7k
views
8 follow
Forum: Recommendation required for solution of computation requirements in Genomics field
DataAnalysis NGS Genomics
updated 4.4 years ago by 45k • written 4.5 years ago by ▴ 350
0
votes
0
replies
714
views
Can I model when 2 population separeted in the past using BEAST?
populationgenetics beast
4.5 years ago by harmadikemil • 0
0
votes
0
replies
928
views
How can I add text label outside the tree in iTOL ?
iTOL annotation tree label
4.5 years ago by anran04100 • 0
4
votes
4
replies
4.8k
views
Samtools sort: too many open files error
samtools sort
updated 4.5 years ago by ★ 1.3k • written 4.5 years ago by ▴ 40
1
vote
0
replies
1.1k
views
Manta SV caller: Why is the ${MANTA_INSTALL_PATH}/bin/configManta.py.ini file missing?
Basespace Manta
4.5 years ago by ilante ▴ 30
0
votes
0
replies
1.2k
views
One-sided test with LDSC --h2 flag and custom annotations
heritability ldsc partitioned
4.5 years ago by gokberk ▴ 90
0
votes
2
replies
2.6k
views
heterogeneity in cluster when using Seurat Doheatmap
scRNAseq cluster r Seurat seurat
4.5 years ago by Jie • 0
45
votes
7
replies
47k
views
9 follow
Any Good Bam And Sam Viewer?
viewer sam bam
updated 3.7 years ago by 45k • written 14.0 years ago by ▴ 170
7
votes
14
replies
4.1k
views
Repeat masking problem
repeatmasking ngs repeatmasker
4.4 years ago by Shri hari ▴ 40
0
votes
0
replies
710
views
Resistome Analyzer Report
bwa metagenomic resistome
4.5 years ago by Bio_Crap • 0
121,904 results • Page 676 of 2439
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Answer: Tried building a compact sequence format with 4-bit storage
Tried building a compact sequence format with 4-bit storage
Shift in RNA 3' position, Term-Seq vs RNASeq
Comment: STARlong for pacbio Isoseq reads
Comment: Automatically annotating a feature using a genbank file
Answer: Is this PCA plot correct??
Answer: Is this PCA plot correct??
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Recent Replies
Comment: Is total miRNA in EV constant? Implications for library size normalization. by Gordon Smyth ★ 8.3k
RNA-seq is very good at relative analyes. It would be straightforward to determine which miRNAs are relatively more abundant, compared to o…
Comment: Tried building a compact sequence format with 4-bit storage by Pranava ▴ 10
Woah!!! Thank you very much, Matthias. I honestly didn't even know some of those existed and I will definitely go through them and try to u…
Answer: Tried building a compact sequence format with 4-bit storage by Matthias Zepper 5.1k
Hello Pranava, Thanks for sharing your repository. Devising a new file format is an interesting undertaking and certainly a task with many…
Answer: Gene Ontology Enrichment with LOC gene IDs in Common Carp (Cyprinus carpio) by GenoMax 153k
`LOC` gene ID's are often assigned to uncharacterized genes and you may not get useful information from databases for them, thus they will …
Comment: Whole Genome Sequencing IG regions by GenoMax 153k
> are the calls I am seeing reliable or should I take them with something of a pinch of salt? Not sure what calls you are referring to but…
Comment: RNA-SEQ where only a subset of genes is of interest by piffelpaff • 0
Sorry to revive this ancient thread but I'm currently discussing the same question with some people in my lab and would love to somebody po…
Answer: STARlong for pacbio Isoseq reads by YuZJ • 0
Hello, you may try deSALT (DOI: 10.1186/s13059-019-1895-9, GitHub: ydLiu-HIT/deSALT) or uLTRA (DOI: 10.1093/bioinformatics/btab540, GitHub:…
Comment: Shift in RNA 3' position, Term-Seq vs RNASeq by acvill ▴ 350
Without knowing the details of the Term-seq method, could the 38 nt shift be accounted for by the difference in the position of the ribosom…
Comment: STARlong for pacbio Isoseq reads by Buffo ★ 2.4k
Thanks, I'll give it a try.
Comment: STARlong for pacbio Isoseq reads by GenoMax 153k
You could give `mapPacBio.sh` from BBMap suite a try while you wait for other answers. That works for reads up to 6 kb. BBMap has a new hom…
Comment: STARlong for pacbio Isoseq reads by Buffo ★ 2.4k
The average is 1.8kb. I was planning to post it on GitHub, but it seems like the repository has been unattended for the last months, so I d…
Comment: Getting just fastqc.zip file? by GenoMax 153k
Yes, You can either use it on command line or use the graphical user interface.
Comment: STARlong for pacbio Isoseq reads by GenoMax 153k
What is the average length of your reads? That error sounds like a bug, so you may want to post that on `STAR` repo as an issue. I assume …
Comment: Getting just fastqc.zip file? by pourhangleila95 • 0
I want to perform fastQC on my data.Do you use fastQC software for doing it?
Comment: Whole Genome Sequencing IG regions by 719 • 0
Sorry for the poor wording of the original post, also should say I really appreciate people taking a moment to look at my post. My main con…
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