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Search: Posts Made By: Marcela Uliano
Forum: General 04-08-2016, 07:23 AM
Replies: 2
Views: 1,637
Posted By Marcela Uliano
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...
Forum: Pacific Biosciences 03-21-2016, 06:02 AM
Replies: 13
Views: 6,508
Posted By Marcela Uliano
Hey guys, I have a related question,...

Hey guys,

I have a related question, although it's different case, maybe you will be able to give me some inputs.
So, I have a hybrid assembly (illumina + pacbio subreads - DBG2OCL) for an...
Forum: Pacific Biosciences 02-29-2016, 04:18 AM
Replies: 0
Views: 1,425
Posted By Marcela Uliano
SSPACE run time - how to improve performance

Hey guys,

I'm denovo assembling a 1Gb mussel genome. And I've
been using PacBio CCS reads and SSPACElong.pl to scaffold my Illumina
assembly with SOAP. It's looking great, but its taking a long...
Forum: Pacific Biosciences 01-29-2016, 05:34 AM
Replies: 3
Views: 2,708
Posted By Marcela Uliano
Kehey and bowhan, I'm sorry for the delay!...

Kehey and bowhan,

I'm sorry for the delay! You were completely right: for the first time run, it must be 0.

It run like a charm and really helped with my repetitive genome!!

Thank you, guys!
Forum: Pacific Biosciences 12-23-2015, 04:17 AM
Replies: 3
Views: 2,708
Posted By Marcela Uliano
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...
Forum: Pacific Biosciences 12-14-2015, 06:47 AM
Replies: 4
Views: 4,147
Posted By Marcela Uliano
Hi GenoMax, I got an answer already: awk...

Hi GenoMax, I got an answer already:

awk '/^S/{print ">"$2"\n"$3}' in.gfa | fold > out.fa

Thank you so so much!
Forum: Pacific Biosciences 12-14-2015, 05:57 AM
Replies: 4
Views: 4,147
Posted By Marcela Uliano
Yes! Its a very new tool! Basically miniasm...

Yes! Its a very new tool!

Basically miniasm takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. (https://github.com/lh3/miniasm)
...
Forum: Pacific Biosciences 12-14-2015, 03:17 AM
Replies: 4
Views: 4,147
Posted By Marcela Uliano
GFA to fasta file

Hey guys!

Can someone help me writing a awk line for extracting FASTA sequences from a GFA file? (I lack programming skills and will take a long time to do it!!)

I've done a miniasm assembly...
Forum: Bioinformatics 10-29-2015, 06:15 AM
Replies: 4
Views: 2,839
Posted By Marcela Uliano
Hi Brian, its a Mollusk! And I have RNA...

Hi Brian, its a Mollusk!

And I have RNA (cDNA) sequenced with 454 and assembled!
Forum: Bioinformatics 10-23-2015, 01:40 AM
Replies: 4
Views: 2,839
Posted By Marcela Uliano
Thank you Brian! Well, I know that the...

Thank you Brian!

Well, I know that the genome I'm assembling has a high amount of repetitive regions and I have the stats for this first draft, its still pretty bad.

The thing is I have some...
Forum: Bioinformatics 10-19-2015, 04:23 AM
Replies: 4
Views: 2,839
Posted By Marcela Uliano
454 reads mapping to more than one scaffold?

Hey guys, I've been struggling with this question for a while, since I don't program very well.

So, I've mapped some 454 contigs to a very fragmented draft genome (a lot of scaffolds), and I would...
Forum: Bioinformatics 07-21-2015, 05:28 AM
Replies: 12
Views: 5,293
Posted By Marcela Uliano
Testing Fahmida's idea

Hey guys, before merging and cutting reads, I decided to test the internal parameter suggested by Fahmida, put a higher FF_MAX_STRETCH, and it worked. I could pass the FillFragments step..

I'll...
Forum: Bioinformatics 07-12-2015, 07:23 AM
Replies: 12
Views: 5,293
Posted By Marcela Uliano
Hey guys, I was wondering if any of you solved...

Hey guys, I was wondering if any of you solved this problem?

I'm having a similar issue "Less than 10% of fragment pairs were filled."

I have about 113 times coverage for the genome with pair...
Forum: Illumina/Solexa 01-07-2015, 07:08 AM
Replies: 1
Views: 1,548
Posted By Marcela Uliano
Sophie's choice: Random mate-pairs or gel selection in Illumina?

Hi guys!

I'm sequencing and assembling a de novo invertebrate genome of about 0,8Gb. I want to make a lane run of Illumina nextera mate-pairs, but I'm having some difficulty on selecting the size...
Forum: General 11-24-2014, 03:20 AM
Replies: 11
Views: 3,616
Posted By Marcela Uliano
Google Cloud Platform

Hey guys!

I was asked to test a little this Google Cloud Platform. I'm just login to free trial, but I would like to have opinions of people who have already used it.
Is it like amazon cloud,...
Forum: Bioinformatics 04-11-2012, 06:08 AM
Replies: 4
Views: 1,656
Posted By Marcela Uliano
Thanks a lot maubp! Ill do that. But you,...

Thanks a lot maubp!

Ill do that. But you, pretty much, have already helped me to solve my doubt!
Forum: Bioinformatics 04-11-2012, 05:40 AM
Replies: 4
Views: 1,656
Posted By Marcela Uliano
Thanks maubp So the quality valeu coming...

Thanks maubp

So the quality valeu coming with the sff file or the one from the fasta format (fna), the .qual are based on PHRED logarithmic scale?
Forum: Bioinformatics 04-10-2012, 07:41 PM
Replies: 4
Views: 1,656
Posted By Marcela Uliano
bioinformatics

Hey guys!

I was wondering how should I interpret the quality scores coming from results from 454 GS jr cDNA (not paired end) reads?

I mean, I read a lot that its prhed-like. But as the...
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