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Search: Posts Made By: panos_ed
Forum: Bioinformatics 01-29-2015, 03:47 AM
Replies: 4
Views: 2,173
Posted By panos_ed
Thank you both guys for the hints! ...

Thank you both guys for the hints!

westerman, I'll give ABySS a go and see what I get.

bioBob, I had tried MaSuRCA about a year ago, but was really disappointed (very, very buggy!). I heard...
Forum: Bioinformatics 01-27-2015, 07:02 AM
Replies: 4
Views: 2,173
Posted By panos_ed
Hybrid assembly using HiSeq and MiSeq data

I'm trying to assemble a relatively large insect genome (~ 1.5 Gbp) and have sequencing data from two different sequencing platforms that I want to combine, in order to get the best possible...
Forum: Bioinformatics 01-07-2015, 03:15 AM
Replies: 19
Views: 29,109
Posted By panos_ed
Why 14bp? Why not something else?

Why 14bp? Why not something else?
Forum: Bioinformatics 02-10-2014, 02:29 AM
Replies: 18
Views: 15,424
Posted By panos_ed
According to this...

According to this (http://supportres.illumina.com/documents/myillumina/9a153ef3-64cc-4408-8dbf-fc0d570d3344/directional_mrna-seq_sampleprep_guide_15018460_a.pdf), directional and strand-specific are...
Forum: Bioinformatics 08-27-2013, 10:37 AM
Replies: 25
Views: 20,813
Posted By panos_ed
Hello Alex! I've downloaded the precompiled...

Hello Alex!

I've downloaded the precompiled binaries for Linux (64bit) and I still get this "index out range" error. In my case, however, the problem appears to be in the "source" field (the...
Forum: RNA Sequencing 10-19-2012, 05:18 AM
Replies: 0
Views: 826
Posted By panos_ed
ORFs in contigs from strand-specific RNA-seq

Hello,

In contigs assembled from strand-specific RNA-seq reads should the ORF be on the plus strand, or could it also be on the minus?

Thanks,
Panos
Forum: Bioinformatics 08-09-2012, 03:25 PM
Replies: 18
Views: 15,424
Posted By panos_ed
Thanks for the info Jim! So if most of the...

Thanks for the info Jim!

So if most of the pairs in a contig contain reads that are like this:

=====>----------<=====
(red) (blue)

then this means that sequencing was...
Forum: Bioinformatics 08-09-2012, 07:30 AM
Replies: 18
Views: 15,424
Posted By panos_ed
Thanks Jim! I selected "first-of-pair" as...

Thanks Jim!

I selected "first-of-pair" as you told me but can't find out what the colors mean (and couldn't find it either in IGV's manual).

Can you please explain what the colors (red, blue...
Forum: Bioinformatics 08-08-2012, 02:32 PM
Replies: 18
Views: 15,424
Posted By panos_ed
How should a strand-specific experiment look like in IGV?

I have a paired-end, strand-specific dataset and used Trinity to assemble the contigs. I then mapped the reads back to the contigs to calculate transcript abundance and viewed the resulting bam file...
Forum: Bioinformatics 08-05-2011, 11:33 AM
Replies: 6
Views: 12,598
Posted By panos_ed
So Velvet is using k-mer coverage values instead...

So Velvet is using k-mer coverage values instead of base coverage in its parameters, right?

In the above example, if my k-mer size is 21 and I want to eliminate all regions with coverage of 2x or...
Forum: De novo discovery 06-13-2011, 09:28 AM
Replies: 82
Views: 47,929
Posted By panos_ed
Celia, I don't know if Trinity is still...

Celia,

I don't know if Trinity is still running but if it is taking too long at the Butterfly step, then you might find interesting this note...
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