User: elisheva

gravatar for elisheva
elisheva100
Reputation:
100
Status:
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Location:
Israel
Last seen:
1 week, 1 day ago
Joined:
3 years, 10 months ago
Email:
e***********@gmail.com

MSc bioinformatics student

 

Posts by elisheva

<prev • 112 results • page 1 of 12 • next >
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Comment: C: Confusion regarding 7th and 8th column of FANTOM5 Enhancer Coordinates BED File
... I read the official paper again and I think I realized ho they set the center. While the start and end coordinates represent the exact CAGE-seq peaks (on opposite strands) the center is calculated as the midpoint between the most left coordinate of the first peak and the rightmost coordinated ...
written 10 weeks ago by elisheva100
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Comment: C: Confusion regarding 7th and 8th column of FANTOM5 Enhancer Coordinates BED File
... I ran into exactly the same problem, reading the Anderson Lab blog and the original paper didn't help. I tried to write to the FANTOM, but didn't get any answer. If you solved this issue, I'd love to hear about it. ...
written 12 weeks ago by elisheva100
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Finding enhancers of the whole human body
... HI! I am looking for enhancer bed files of the whole human body. I found at Fantom5 available data, but I am not sure how they define it and if they can be trusted. The Enhancers Atlas has data for a specific cell line or tissue and I guess that downloading all the data and combine it af ...
fantom5 enhancers cage-seq written 4 months ago by elisheva100
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Comment: C: Retrive gene sequences of all ensembl organsims
... Thanks a lot, I deeply appreciate your response. Is there any course or tutorial to study how to work with the Perl API? I am completely new to this thing (for Perl in general), I couldn't understand how to download the sequences by retrieving GFF file by reading the documents at t ...
written 6 months ago by elisheva100
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Comment: C: Retrive gene sequences of all ensembl organsims
... I know, that exactly what I did before. The problem is that there are no gene sequences at the FTP site but only whole genome or cDNAs. ...
written 6 months ago by elisheva100
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Retrive genomic sequences of genes of all ensembl organsims
... Hi everyone I am trying to download gene sequences of **all** Ensembl organisms in fasta format including: Vertebrates, Metazoa, Plants, Fungi, Bacteria and Protists In the past I worked only with vertebrates, therefore I downloaded the whole genome and the matching gff file via ens ...
gene ensembl sequence sequencing ftp written 6 months ago by elisheva100
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Extract the sequence of retrotransposons sites
... Hello I am trying to locate the AT-rich sites of retrotransposons. I downloaded the repeats table from the genome browser with all transposable elements (hg38, RepeatMasker track). I thought to filter the file to extract only SINE and LINE coordinates. However, I have no id ...
genome retrotransposons ucsc written 6 months ago by elisheva100
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Comment: C: What is P value and Padj value in DEGs ?
... I recommend you to read this tutorial: https://bioc.ism.ac.jp/packages/2.14/bioc/vignettes/DESeq2/inst/doc/beginner.pdf ...
written 8 months ago by elisheva100
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Comment: C: HTSeq-count: gene models/transcripts are in FASTA format not gtf/gff
... Which reference genome did you use? I am sure you can get the matching gtf/gff files somewhere. ...
written 8 months ago by elisheva100
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Comment: C: Convert regex into DNAString object
... Because I use StringSet and I want the analysis to be as fast as possible. If I will convert any single interval into character, I guess it will be much slower. ...
written 13 months ago by elisheva100

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