User: marcela.uliano

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30
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New User
Location:
European Union
Website:
http://improvisocienti...
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MahUliano
Last seen:
12 months ago
Joined:
2 years, 5 months ago
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m*************@gmail.com

Posts by marcela.uliano

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Tabix With Gff3
... Oh sorry, Pierre! I'll do that! ...
written 12 months ago by marcela.uliano30
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Answer: A: Tabix With Gff3
... Hey guys! Sorry about the simplicity of the question! But I'm trying for ours to open a gff in artemis to check some gene models and I can not!! The fasta and sorted bam file work well, but I can not get the gff together at all!! So, I tried to sort and index it with tabix, but its not working! ...
written 12 months ago by marcela.uliano30
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Comment: C: Parsing genomeCoverageBed (-bga flag) result to see multiple contigs coverage!
... Thanks, Devon! I'll have a look! I was also thinking in a simple solution: maybe just using 'samtools indxstat' with my bam file. I wont have information of coverage per base, but I'll have size of contig and number of reads mapped, so a raw estimate I can do from there. I'll play around with diff ...
written 13 months ago by marcela.uliano30
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Parsing genomeCoverageBed (-bga flag) result to see multiple contigs coverage!
... Hey guys! I'm trying to calculate one thing and I'm sure someone else has also done this. So maybe someone have a script ready! I have a draft de novo genome, and augustus predicted too many genes (54 thousand), so I've aligned my RNA-seq to the exons predicted to discharge the exons with bad (5 o ...
genome alignment sequence rna-seq written 13 months ago by marcela.uliano30
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Comment: A: SNP calling for correcting errors ?
... Thank you Ih3 and ALchEmiXt, Running PILON iteractively is exactly what I'm doing and its working great! I notice by the number of CEGs I got in the draft genome previous and post PILON. Thanks guys! ...
written 17 months ago by marcela.uliano30
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SNP calling for correcting errors ?
... Hey guys, Let's say one has scaffolded a draft genome with PacBio subreads and PB Jelly, but still is concerned about not enough coverage of Illumina contigs, and the maintenance of PacBio indel errors in the final draft. This person also have high quality RNA-seq illumina and can map this to the ...
genome assembly alignment rna-seq snp written 17 months ago by marcela.uliano30
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Problem to install the package BCBio from biopython - not available?
... Hey guys! I have a exonarate gff result and I'm trying to covert it to gb format, so I can train ausgustus! The thing is I've found this script https://github.com/robsyme/nextflow-annotate/blob/master/bin/gff2gb but I'm having a dependency with the BCBio from Biopython. I've been trying to instal ...
genome next-gen alignment rna-seq written 19 months ago by marcela.uliano30
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Run Quiver for hybrid assembly?
... Hey guys, I have a hybrid assembly (illumina + pacbio subreads - DBG2OCL assembler) for an 1.5Gb eukaryotic genome, and now I'm in doubt if I should quiver this assembly or not. Once, as I read, quiver calls consensus based on the pacbio quality of the aligned subreads to the draft genome, what i ...
genome assembly alignment written 20 months ago by marcela.uliano30 • updated 20 months ago by rhall160
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DBG2OLC - parameter f cannot identify my PacBio reads
... Hi guys! I'm trying to run DBG2OLC with contigs built with platanus + 13x times genome coverage in PacBio subreads (fastq). But looks like the parameter f don't understand my PacBio reads. Do I have to create any kind of info file to unpload to the f parameter? My command is: ./DBG2OLC LD 1 Contig ...
software error assembly dbg2olc pacbio genome written 23 months ago by marcela.uliano30 • updated 19 months ago by Rohit1.3k
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Comment: A: GFA to Fasta file
... Awesome!!   Thank you so much!     ...
written 23 months ago by marcela.uliano30

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