User: matija.sosic

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matija.sosic90
Reputation:
90
Status:
New User
Location:
Croatia/Zagreb/Faculty of Electronical Engineering and Computing
Last seen:
5 years, 11 months ago
Joined:
7 years, 1 month ago
Email:
m***********@gmail.com

Computer science student doing his master's - identifying organisms from metagenomic sample. Contributes to bioinformatics.

Posts by matija.sosic

<prev • 15 results • page 1 of 2 • next >
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documented metagenomic RNA-SEQ data
... I am interested in metagenomic RNA-SEQ data. It would be great if it its analysis is publicly available so I can validate my analysis against it. So far I have found: http://www.hmpdacc.org/RSEQ/ Thank you!   ...
data metagenomics rna-seq written 6.0 years ago by matija.sosic90
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Comment: C: Where can I find genome of a single bacteria?
... I have one fasta file from that strain, but also this one: http://www.ncbi.nlm.nih.gov/sra/?term=SRR1187101 Is there some way to know if this strain's genome is sequenced, besides checking manually al sources? Would it be ok if I just aligned to tthe strain you proposed? Thanks! ...
written 6.1 years ago by matija.sosic90
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Where can I find genome of a single bacteria?
... Where can I find genome of a single bacteria, e.g. of E.coli? I downloaded rna-seq reads of E.coli from SRA and now I would like to align it using BWA to the genome of E.coli. ...
genome bacteria written 6.1 years ago by matija.sosic90 • updated 3.3 years ago by Hajk-Georg Drost140
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What is the difference between GEO and SRA ncbi databases?
... I found that GEO holds "processed sequence data files", while SRA holds "raw sequence data files". In which way processed? I am interested in rna-seq bacterial data, is GEO right resource for me? ...
geo sra ncbi written 6.1 years ago by matija.sosic90 • updated 6.1 years ago by Chris Fields2.1k
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Comment: C: Where can i find some bacterial RNA-Seq data?
... Thanks, this looks great! Do you maybe know how to find out how long are the reads? I tried first result with 36bp, that seems really short to me. Also, when I use fastq-dump to get .fastq file almost half of each read is 'N'. ...
written 6.1 years ago by matija.sosic90
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Where can i find some bacterial RNA-Seq data?
... Where can i find some bacterial RNA-Seq data, e.g. of Escherichia Coli? I would like to analayse single bacteria's transcriptome to see which genes get expressed. ...
rna-seq bacterial written 6.1 years ago by matija.sosic90 • updated 6.1 years ago by geek_y11k
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Are There Certain Proteins (Cdss) Of Bacteria Which Get Expressed In Transcriptome More Than Others?
... So what I am doing: I am analyzing sequenced transcriptome of eukaryotic host + bacterias. Host is known in advance, and goal is to identify pathogens. I'm interested if it is possible to identify those bacterias by their CDSs found in that transcriptome. For example, is it possible to identify bac ...
cds bacteria protein transcriptome written 6.2 years ago by matija.sosic90 • updated 6.2 years ago by biotech540
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Answer: A: Megan 5 - How To Extract All Read Assignments To A Dsv
... Select Tree -> uncollapse all and then press ctrl + a to select all nodes. Having all nodes selected, File -> Export -> DSV Format will export all of them. ...
written 6.4 years ago by matija.sosic90
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Megan 5 - How To Extract All Read Assignments To A Dsv
... I would like to export assignment of each read to taxon_id (from NCBI tree). When I go to File -> Export -> DSV Format, and then choose format "read-name, taxon-id" I have to select some node otherwise 0 lines are written to file. Also when I collapse subtree, all assignments of a subtree are ...
written 6.4 years ago by matija.sosic90
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Comment: C: Generate Uniform, Perfect Short Reads From Genome
... why don't you try metasim? It's for metagenomics but can also generate reads from a single genome. And you can choose option that applies non errors, and uniform length ...
written 6.4 years ago by matija.sosic90

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Supporter 6.0 years ago, voted at least 25 times.
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