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Search: Posts Made By: francicco
Forum: Bioinformatics 08-04-2016, 04:05 AM
Replies: 3
Views: 3,227
Posted By francicco
I fix this compiling augustus with gcc/5.3.0

I fix this compiling augustus with gcc/5.3.0
Forum: Sample Prep / Library Generation 04-22-2015, 07:12 AM
Replies: 16
Views: 4,694
Posted By francicco
Actually I would like not to use PCRs...

Actually I would like not to use PCRs...
Forum: Sample Prep / Library Generation 04-17-2015, 06:19 AM
Replies: 16
Views: 4,694
Posted By francicco
Hi guys, the genomes I'm working with ranges...

Hi guys,

the genomes I'm working with ranges from 300 to 500Mb.

It looks clear Nextera XT is not very suitable. So far ThruPLEX looks better. Do you guys agree?

thanks
F
Forum: Sample Prep / Library Generation 04-09-2015, 11:54 PM
Replies: 16
Views: 4,694
Posted By francicco
Thank you K. So which kit do you would...

Thank you K.

So which kit do you would suggest? Or which company...

F
Forum: Sample Prep / Library Generation 04-09-2015, 12:37 PM
Replies: 16
Views: 4,694
Posted By francicco
Thanks!!! What about ThruPLEX...

Thanks!!!

What about ThruPLEX (http://rubicongenomics.com/products/thruplex-dna-seq-kit/) DNA-seq Kit?

F
Forum: Sample Prep / Library Generation 04-09-2015, 06:54 AM
Replies: 16
Views: 4,694
Posted By francicco
Ultra-low DNA yield library prep.

Dears all,

We're about to sequence a genome from a small insect. We can get ~500-1000 ng from 5 pooled individuals. But giving wild population should have high, maybe too high variability, we...
Forum: Bioinformatics 03-30-2015, 10:40 AM
Replies: 0
Views: 1,476
Posted By francicco
Cool FreeBayes not standard haplotype calling

Dear,

It's the first time I'm trying to perform this type of analysis, and I'm not in a standard situation. Here's what I have.

I have a:
- Metagenome reference. Each contig of the reference...
Forum: Bioinformatics 11-11-2014, 02:54 AM
Replies: 1
Views: 1,806
Posted By francicco
I have the same problem, did you solve it?

I have the same problem, did you solve it?
Forum: Bioinformatics 10-29-2014, 01:37 AM
Replies: 11
Views: 3,164
Posted By francicco
Hi guys, I'm also trying to use MaSuRCA to...

Hi guys,

I'm also trying to use MaSuRCA to assembly a Drosophila species, since SOAPdenovo and IDBA-UD fail giving me a N50 smaller than 1k. It looks like MaSuRCA some problem.

These are my...
Forum: Illumina/Solexa 10-20-2014, 12:28 AM
Replies: 9
Views: 1,769
Posted By francicco
I can tell you, they are the same ...

I can tell you, they are the same

http://en.wikipedia.org/wiki/Jumping_library

"[...] mate-pair sequencing, which is basically a combination of Next Generation Sequencing with jumping...
Forum: Illumina/Solexa 10-20-2014, 12:17 AM
Replies: 9
Views: 1,769
Posted By francicco
Maybe I did wrong but, I understood that JUMP...

Maybe I did wrong but, I understood that JUMP stands for jumping libraries, so mate pairs. Is it wrong?
Forum: Illumina/Solexa 10-20-2014, 12:03 AM
Replies: 9
Views: 1,769
Posted By francicco
Hi guys, Thanks for your help, really...

Hi guys,

Thanks for your help, really appreciated. So, fastqc profiles are attached (fastqc_data_R1-2.zip).

My species is D. nigrosparsa. The closely related species for which a genome is...
Forum: Illumina/Solexa 10-17-2014, 06:25 AM
Replies: 9
Views: 1,769
Posted By francicco
Failed Genome assembly

Dears,

I'm trying to assemble the genome of a Drosophila species, but I'm having serious problem.

I have 4 illumina libraries: 1 paired-end library: 100bp, insert size 300bp; 3 MP libraries:...
Forum: Bioinformatics 09-18-2014, 12:51 AM
Replies: 1
Views: 1,758
Posted By francicco
I have se same question!

I have se same question!
Forum: Bioinformatics 09-12-2014, 08:15 PM
Replies: 4
Views: 1,503
Posted By francicco
Actually it is a cluster. I'm installing...

Actually it is a cluster. I'm installing libraries and application on local.
Forum: Bioinformatics 09-12-2014, 12:07 PM
Replies: 4
Views: 1,503
Posted By francicco
Thanks, the code gave me: attempt to...

Thanks,

the code gave me:

attempt to open /usr/x86_64-suse-linux/lib64/libexpat.so failed
attempt to open /usr/x86_64-suse-linux/lib64/libexpat.a failed
attempt to open...
Forum: Bioinformatics 09-12-2014, 07:03 AM
Replies: 4
Views: 1,503
Posted By francicco
Compilation of AMOS [-lexpat error]

Dears,

I'm trying to compile AMOS package. Unfortunately I'm having this error:

g++ -g -O2 -o toAmos_new toAmos_new-toAmos_new.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a...
Forum: Bioinformatics 07-18-2014, 02:23 AM
Replies: 24
Views: 15,362
Posted By francicco
Thank you very much guys. F

Thank you very much guys.
F
Forum: Bioinformatics 07-18-2014, 01:43 AM
Replies: 24
Views: 15,362
Posted By francicco
I'm trying to do it on a Drosophila mtDNA.

I'm trying to do it on a Drosophila mtDNA.
Forum: Bioinformatics 07-18-2014, 01:23 AM
Replies: 24
Views: 15,362
Posted By francicco
Anyway, any help about this issue? F

Anyway, any help about this issue?

F
Forum: Bioinformatics 07-18-2014, 12:57 AM
Replies: 24
Views: 15,362
Posted By francicco
Well, definitely not. But mtDNA is quite smaller...

Well, definitely not. But mtDNA is quite smaller than the nuclear genome; it's a single molecule while nuDNA has chromosomes; mtDNA genes do not splice or have different isoforms. I'd say is a...
Forum: Bioinformatics 07-17-2014, 11:49 PM
Replies: 24
Views: 15,362
Posted By francicco
@Jeremy. I think that the protocol works pretty...

@Jeremy. I think that the protocol works pretty well, and the way MIRA and MITObim work is not contrary to situation in which you do not have a complete coverage on the molecule. But maybe @maubp can...
Forum: Bioinformatics 07-17-2014, 02:24 PM
Replies: 24
Views: 15,362
Posted By francicco
Dears, I found this thread interesting and I'm...

Dears, I found this thread interesting and I'm trying to use this procedure.
I have 140M RNAseq reads in paired-ends (140M+140M) too much. MIRA give me clear warning, too much coverage. So I'm...
Forum: Bioinformatics 07-04-2014, 02:57 AM
Replies: 1
Views: 1,472
Posted By francicco
mtDNA de-novo assembly

Dear assemblers,

I'm trying to assemble the complete mtDNA genome of a Drosophila species using pair-ends transcriptome reads. To do so I'm using MIRA 4 with MITObim 1.7 following the protocol...
Forum: Bioinformatics 05-22-2012, 08:54 AM
Replies: 46
Views: 19,894
Posted By francicco
I personally do not trust cufflinks 2 results....

I personally do not trust cufflinks 2 results. For instance it gives 0 FPKM to transcript clearly expressed

Developers need to do something, sooner or later...
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