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Forum: Bioinformatics 07-27-2016, 04:59 AM
Replies: 2
Views: 1,474
Posted By chariko
Perfect!! Genomax Thank you very much for...

Perfect!!

Genomax Thank you very much for your response.
Forum: Bioinformatics 07-27-2016, 04:48 AM
Replies: 2
Views: 1,474
Posted By chariko
Strange Illumina fastq header

Hi all,

I have received two paired end fastq files to analyze and when I look at the header I realized the following:

File 1
@HWI-ST1131:130302:D1RGUACXX:6:1101:1133:2071 1:N:0:
...

File 2...
Forum: Bioinformatics 07-25-2016, 06:33 AM
Replies: 0
Views: 1,123
Posted By chariko
RnaSeq vs Microarray correlation

Hi all,

I have an experiment with 80 samples both of them run with microarray and RnaSeq. I want to correlate the results between the two technologies.

I received the results from the RnaSeq...
Forum: Metagenomics 12-04-2015, 06:13 AM
Replies: 5
Views: 1,929
Posted By chariko
thanks colindaven for your answer, do you have...

thanks colindaven for your answer, do you have any reference in which this percentages are showed?
Forum: Metagenomics 12-04-2015, 03:28 AM
Replies: 5
Views: 1,929
Posted By chariko
51% of Bacteroides vulgatus whose habitat is...

51% of Bacteroides vulgatus whose habitat is distal small intestine of humans.
10% of Bacteroides thetaiotaomicron a dominant member of our normal distal intestinal microbiota
9% Porphyromonadaceae...
Forum: Metagenomics 12-03-2015, 09:04 AM
Replies: 5
Views: 1,929
Posted By chariko
Viral metagenomics sample with a high concentration of bacteria

Hi all,

I have analyzed a total of 7 samples coming from the bacteriophage fraction of human faeces. Purification included resuspension of the sample in buffer SM and homogenized sample was then...
Forum: Sample Prep / Library Generation 11-26-2015, 12:44 AM
Replies: 8
Views: 2,453
Posted By chariko
As I told before I finally tried out the Corning...

As I told before I finally tried out the Corning Spin-X columns and they worked perfect for me. Anyway, just because this colums are just for broking the gel and get the DNA through the tubes I think...
Forum: Illumina/Solexa 09-01-2015, 06:51 AM
Replies: 16
Views: 10,300
Posted By chariko
Hi Huguesparri, I checked Spin-X from Costar...

Hi Huguesparri,

I checked Spin-X from Costar (http://www.sigmaaldrich.com/labware/labware-products.html?TablePage=17192542) and they only have 0.22 or 0.45 um filter tubes. Illuminaīs...
Forum: Sample Prep / Library Generation 08-28-2015, 12:52 AM
Replies: 8
Views: 2,453
Posted By chariko
Thanks kerplunk412 and nucacidhunter for your...

Thanks kerplunk412 and nucacidhunter for your answers.

I didnīt know about production defect for those Illuminaīs recommended tubes, this reaffirms my intention of changing the tubes. Also,...
Forum: Sample Prep / Library Generation 08-27-2015, 01:56 AM
Replies: 8
Views: 2,453
Posted By chariko
Post miRNA Truseq 5 μm filter tube size alternative

Hi all,
I am planning to run a small RNA Seq (TruSeq Small RNA Library Prep) in a Illumina MiSeq and reading the protocol they use a 5 um filter tube to transfer the elute and the gel debris...
Forum: Sample Prep / Library Generation 06-11-2015, 02:26 AM
Replies: 48
Views: 25,376
Posted By chariko
Thanks for your answer I will take a look at your...

Thanks for your answer I will take a look at your paper (reference?).

Anyway, DNA was quantified with Qubit prior to being diluted so I suppose everything was correct but I will check it again......
Forum: Sample Prep / Library Generation 06-09-2015, 05:51 AM
Replies: 48
Views: 25,376
Posted By chariko
I am having a similar problem with my experiment...

I am having a similar problem with my experiment so I hope someone can give me a clue.

I'm making Nextera XT libraries of some phago genomic DNA samples following protocol instructions. Samples...
Forum: De novo discovery 05-07-2015, 12:42 AM
Replies: 3
Views: 1,494
Posted By chariko
Smile You are right, I got there the answer. Anyway the...

You are right, I got there the answer. Anyway the answer on how to join the caf files was as easy as:

cat file1.caf file2.caf >combined.caf
Forum: De novo discovery 05-06-2015, 04:12 AM
Replies: 2
Views: 1,587
Posted By chariko
Regarding your questions: 1) If you want to...

Regarding your questions:

1) If you want to trim your sequences (actually I do not recommend it at all) you could use prinseq (http://prinseq.sourceforge.net/) which actually works very well and...
Forum: De novo discovery 05-06-2015, 03:44 AM
Replies: 3
Views: 1,494
Posted By chariko
MIRA de novo assembly with reference genome doubt

Hello everybody,

I recently downloaded Mira software and I am getting some doubts I hope someone can help me to resolve.

My experiment consists in a paired end Illumina de novo assembly having...
Forum: RNA Sequencing 04-21-2015, 09:15 AM
Replies: 3
Views: 2,071
Posted By chariko
Thanks a lot for your answer, mbblack. You are...

Thanks a lot for your answer, mbblack. You are right, that was my case.
Forum: RNA Sequencing 04-21-2015, 08:24 AM
Replies: 3
Views: 2,071
Posted By chariko
Strange results Deseq2 no adjusted p values or even p values

I analyzed a RNASeq experiment with EDGE-Pro and the statistical test was performed with Deseq2.
I obtained the following strange results for the statistical test for some genes (info regarding the...
Forum: Bioinformatics 03-02-2015, 02:25 AM
Replies: 0
Views: 1,066
Posted By chariko
Edge-pro error

Hi all,

I recently downloaded the software EDGE_pro_v1.3.1 and when trying to run it:


OMP_NUM_THREADS=6
edge.pl -g genome_SL1344.fasta -p genome_SL1344.ptt -r genome_SL1344.rnt -u...
Forum: Ion Torrent 02-06-2015, 12:53 AM
Replies: 2
Views: 1,450
Posted By chariko
The fact is if you want to detect rare variants...

The fact is if you want to detect rare variants or just doing a normal differential expression analylisis. Also if you include biological replicates (highly recommended 3 replicates per condition)for...
Forum: Bioinformatics 12-17-2014, 05:20 AM
Replies: 7
Views: 2,701
Posted By chariko
I am getting the same error: velveth 21 21...

I am getting the same error:

velveth 21 21 -reference Reference.fna -shortPaired -sam 1D14.sam

[0.000001] Reading FastA file Reference.fna;
[1.264527] 90 sequences found
[1.264545] Done...
Forum: Bioinformatics 11-21-2014, 08:58 AM
Replies: 12
Views: 4,430
Posted By chariko
I could finally run the program when I put all my...

I could finally run the program when I put all my files in the CISA1.3 folder. I still don't know why it does not work in their original folder but at least it worked.

Thanks a lot
Forum: Bioinformatics 11-21-2014, 08:32 AM
Replies: 12
Views: 4,430
Posted By chariko
Thank you very much for your comment. I did it...

Thank you very much for your comment. I did it and now I got the following error:

CISA.config
CISA1....
Contigs: 2013
Whole_Genome: 0
Ref0.fa and Query0.fa start to run NUCmer!
Done!...
Forum: Bioinformatics 11-21-2014, 08:18 AM
Replies: 12
Views: 4,430
Posted By chariko
I am having the same problem but after putting...

I am having the same problem but after putting the way after running the command which it continues not working.

Thatśs my CISA config file:

genome=7000000
infile=1D14_Merged.ctg.fa...
Forum: Bioinformatics 11-21-2014, 06:57 AM
Replies: 1
Views: 849
Posted By chariko
Soap de novo Input file for CISA

I want to use CISA but I am not sure about the files I have to input.

My question is regarding the SOAP results. Do I have to use just the scaffolds, scaffolds and contigs or only contigs.

Any...
Forum: Genomic Resequencing 10-27-2014, 09:09 AM
Replies: 0
Views: 1,111
Posted By chariko
Negative start position bed file

I aligned two samples (bwa; filter with samtools, removed duplicates with picard-tools, bamtobed and bed to bedgraph with genomeCoverageBed) to a genome file consisting in 4 genes and the first...
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