User: tonu.margus

gravatar for tonu.margus
tonu.margus20
Reputation:
20
Status:
New User
Location:
Sweden, Umeå, Umeå University
Last seen:
2 years, 3 months ago
Joined:
3 years, 3 months ago
Email:
t**********@gmail.com

Studying translation dynamics in yeast and using ribosomal-profiling (Ribo-seq) as a method. 

Posts by tonu.margus

<prev • 5 results • page 1 of 1 • next >
0
votes
0
answers
734
views
0
answers
3 frame translation with underling CDS shown on codon wise
... Hi, I am looking for tool for 3 frame translation with some additional formatting/display functionality. There is a bunch of tools/programs for 1, 3 or 6 frame translation (for example http://molbiol-tools.ca/Translation.htm) but all of them are missing what I am looking for. I want 2 things: ...
gene alignment translation written 2.6 years ago by tonu.margus20
0
votes
3
answers
1.3k
views
3
answers
Answer: A: Is there any tools to predict all possible uORFs in an organisms?
... It's a bit late reply but have you become across with ORF-RATER. Authors claim that they approach is very good for discovering small ORF's like uORFs. It utilise Riob-Seq data obtained by initiation inhibitors like Harringtonine (Harr) and lactimidomycin (LTM) in addition to CHX and non treated but ...
written 2.6 years ago by tonu.margus20
0
votes
5
answers
1.9k
views
5
answers
Answer: A: What tools were used to draw these phylogenetic trees?
... There is an ETE toolkit what is a Python framework for the analysis and visualization of trees. It contains multiple tools and pipelines. Homepage is here http://etetoolkit.org/ ...
written 2.7 years ago by tonu.margus20
1
vote
2
answers
1.4k
views
2
answers
Comment: C: How to split genome coverage by read length in Ribo-Seq data
... Hi Tom, Splitting BAM file was one possible way to go. I had to change it a bit to get output in compressed BAM. Here is an example what worked for me to generate 27 nt bam. samtools view -h my.bam | awk 'BEGIN {FS="\t"}; ((/^@/) || (length($10) == 27)) {print $0}' | samtools view -bS - > ...
written 3.2 years ago by tonu.margus20
3
votes
2
answers
1.4k
views
2
answers
How to split genome coverage by read length in Ribo-Seq data
... I am looking for an efficient/simple way for extracting genome coverage for each strand(+/- ) in a given range (for example 25-34) of read length. My input is sorted BAM file (Ribo-Seq data) and as a measure of coverage I would like to get 5' positions of each read. I found `bedtools genomecov` so ...
forum rna-seq written 3.2 years ago by tonu.margus20 • updated 3.2 years ago by EVR540

Latest awards to tonu.margus

Autobiographer 3.2 years ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1328 users visited in the last hour