User: epaminonda

gravatar for epaminonda
epaminonda10
Reputation:
10
Status:
New User
Location:
United Kingdom
Last seen:
1 day, 8 hours ago
Joined:
5 years ago
Email:
g**************@yahoo.it

Posts by epaminonda

<prev • 10 results • page 1 of 1 • next >
0
votes
1
answer
126
views
1
answers
Comment: C: Improving reference gtf annotation via merging with alternative gtf annotations
... Hi, thanks so much for this - I've installed it and run it and it seems it does exactly what I'm after. I was just wondering whether you're one of the developers or maintainers and could ask you a few follow up questions? The main one would be, it seems the tool returns a gff3 containing the uni ...
written 6 weeks ago by epaminonda10
0
votes
2
answers
7.5k
views
2
answers
Comment: C: How To Merge Gff Files
... I have also found that gffcompare removes everything except 'exon' and 'transcript'. Has anyone found out why? Any alternative tools for doing this? ...
written 6 weeks ago by epaminonda10
2
votes
1
answer
126
views
1
answer
Improving reference gtf annotation via merging with alternative gtf annotations - how?
... Hi I am looking at the Ensembl V100 gtf annotation file for one model animal of interest and found the annotation lacks a number of important genes, most crucially human homologues. Interestingly, alongside the reference annotation for this species a few alternative annotations are available in gtf ...
gtf gff3 merge gene annotation written 6 weeks ago by epaminonda10
0
votes
0
answers
367
views
0
answers
Estimating sequence complexity of DNA sequence from fasta file
... Hi I have mapped some pacbio reads to a mammal reference and I am now focusing on understanding the coverage in a ~5Mb region of interest. It seems the majority of the region is well covered by reads. However, a locus of about 500kb in the centre of the region has no reads mapping to it at all. I ...
"repeatmasker" sequence pacbio written 21 months ago by epaminonda10
0
votes
1
answer
675
views
1
answers
Answer: A: Tissue-specific Histone Mark bam files?
... Answering some of my own questions - I found the following portal to be quite useful to assess availability of tissue specific histone mark data [Cistrome DB][1] [1]: http://cistrome.org/db It seems to return results coming from both large scale studies (ENCODE+Roadmap Epigenomics) and small ...
written 2.3 years ago by epaminonda10
0
votes
1
answer
1.6k
views
1
answers
Comment: C: NIH roadmap epigenomics data Bam files
... Hi, I was hoping you could help - I'd like to know if you then solved this by going ahead and converting the tagAlign to bam files, or eventually found the original bams or something else entirely? ...
written 2.3 years ago by epaminonda10
0
votes
1
answer
675
views
1
answer
Tissue-specific Histone Mark bam files?
... Hi everybody A colleague has developed a machine learning tool to perform enhancer prediction based on histone mark ChIP-seq data. I would like to test the tool by performing enhancer calling in a tissue-specific fashion, and I'm looking for publicly available histone modification ChIP-seq data. ...
chip-seq encode epigenomics roadmap histone written 2.3 years ago by epaminonda10
1
vote
1
answer
1.2k
views
1
answer
Sources Of Publicly Available Human Rare Disease WES/WGS Data
... Hi, I was wondering if there are any repositories of WGS/WES for rare human diseases, apart from the DDD dataset. I imagine there will probably be a variety of publications each focusing on a particular disease - if so are people aware of an aggregating resource for rare disease where I could quick ...
genome data wes sequencing wgs written 4.4 years ago by epaminonda10 • updated 4.4 years ago by mastal5112.0k
0
votes
2
answers
4.6k
views
2
answers
Comment: C: Position Frequency Matrix to Position Weight Matrix, whose colsums need to be 1.
... Hi, thanks for this. Did you find an answer to the issue above? Also, could you recommend the best way to obtain PWMs from the Jaspar collection of pfms? ...
written 4.6 years ago by epaminonda10
1
vote
0
answers
2.4k
views
0
answers
SNP enrichment analysis - alternatives to BROAD SNPsnap?
... Hello, I am trying to carry out a SNP genomic enrichment analysis and I was hoping you could help. Basically, I have the following two sets of SNPs: -set_A: 1,695 foreground SNPs. These are 1000g variants which, in addition, are QTL for a trait I'm interested in. They all are within ChIP-seq peak ...
chip-seq snp written 5.1 years ago by epaminonda10

Latest awards to epaminonda

Popular Question 11 months ago, created a question with more than 1,000 views. For Sources Of Publicly Available Human Rare Disease WES/WGS Data
Scholar 2.3 years ago, created an answer that has been accepted. For A: Tissue-specific Histone Mark bam files?
Popular Question 4.1 years ago, created a question with more than 1,000 views. For SNP enrichment analysis - alternatives to BROAD SNPsnap?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1353 users visited in the last hour