User: Panos

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Panos1.6k
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Posts by Panos

<prev • 88 results • page 1 of 9 • next >
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Comment: C: Training Augustus for Maker
... I know it's been a really long time since this was posted but I had to deal with this myself a couple of days ago. So, the Augustus training parameters generated by BUSCO when you use the `--long` option, are saved in the current working directory (i.e. the directory from which you called BUSCO); t ...
written 5 months ago by Panos1.6k
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Assembly Strategy
... We're working on sequencing some big insect genomes (>2GBp) and as the first data comes out, I'm trying to find a way to tackle with them. MaSuRCA crashed on just one lane of unfiltered sequences (~(140 x 2) mil reads) and I started looking for alternatives, since for some of our insects we have ...
illumina written 4.5 years ago by Panos1.6k • updated 4.5 years ago by Charles Warden5.1k
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Comment: C: Data Management System For Bioinformatics?
... I think that's a good solution for managing the sequencing data, although it doesn't look like it can manage assemblies or annotation of that data. Thanks Pierre! ...
written 4.6 years ago by Panos1.6k
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Comment: C: Data Management System For Bioinformatics?
... Thanks for mentioning those posts Ying. I hadn't seen the one about LIMS. ...
written 4.6 years ago by Panos1.6k
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Comment: C: Data Management System For Bioinformatics?
... Thanks for the input! I didn't mean to add each individual read in the database! I just want to be able to download the fastq files of each run. As for the assembly/annotation handling, what I want is to be able to keep, for example, different assembly versions (eg uncorrected and corrected version ...
written 4.6 years ago by Panos1.6k
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Data Management System For Bioinformatics?
... We're planning to do a great deal of Illumina sequencing (several insects) in our lab and I was looking at data management systems that will be able to handle all this data (raw reads, assemblies, annotations, etc). From what I've found so far it looks like the Sequence Retrieval System is doing exa ...
written 4.6 years ago by Panos1.6k • updated 4.6 years ago by Pierre Lindenbaum111k
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Comment: C: Possible Gene Unflattening Error In Bp_Genbank2Gff3.Pl Bioperl Script
... Thanks for the advice Emily! Why is gtf2gff3 outputting an unsorted gff file, though? Does it, at least, keep the features of a gene (like CDSs, exons, etc) right after each gene? ...
written 4.8 years ago by Panos1.6k
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Possible Gene Unflattening Error In Bp_Genbank2Gff3.Pl Bioperl Script
... I want gff3 files for certain Vertebrates, but I could only find the corresponding genbank files in Ensembl. So I decided to download them and convert them to gff3, using the bioperl script bp_genbank2gff3. Even though it produces a gff3 file, I get an error and I'm not sure if the resulting file is ...
gff3 ensembl bioperl genbank conversion written 4.8 years ago by Panos1.6k • updated 4.8 years ago by Emily_Ensembl15k
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Comment: C: How To Blast A Nucleotide Profile (Pssm) Against A Nucleotide Database?
... I'm guessing you haven't used the matrix for searching a BLAST-formatted, nucleotide database, right? If you did, what program you used? ...
written 4.9 years ago by Panos1.6k
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Comment: C: How To Blast A Nucleotide Profile (Pssm) Against A Nucleotide Database?
... So what did you do with the matrix? In my case, I want to blast it against a nucleotide database. Did you also do something like this? ...
written 4.9 years ago by Panos1.6k

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