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Forum: General 04-21-2016, 01:39 AM
Replies: 7
Views: 10,346
Posted By mcastro
SRA errors uploading fastq files

Hi all,

I was trying to upload several human exomes (fastq files) to SRA but I have several problems and I couldn't obtain and answer from sra so I would like to ask if anybody had the same...
Forum: Bioinformatics 04-14-2014, 09:22 AM
Replies: 14
Views: 10,214
Posted By mcastro
BRIG error in multi-fasta tutorial

I have the same problem when I try with multi-fasta example tutorial. I get this error:
java.lang.IllegalArgumentException: Comparison method violates its general contract!
Forum: RNA Sequencing 09-03-2012, 04:34 AM
Replies: 0
Views: 1,640
Posted By mcastro
Unusual small FPKM Cufflinks values


Recently I obtained some expression results for a standard RNAseq anaysis in human samples. I'm surprised by these results because almost all FPKM values are in the range 10e-5 - 10e-7. I...
Forum: RNA Sequencing 08-02-2012, 07:21 AM
Replies: 2
Views: 2,312
Posted By mcastro
Viral genome assembly from RNA-seq data


I'm performing a RNA-seq analysis from a virus infected plant. After mapping the Illumina Hiseq paired reads against the plant genome, I used the unmapped reads to blast the virus genome...
Forum: Bioinformatics 06-08-2012, 12:42 PM
Replies: 6
Views: 4,060
Posted By mcastro
Hi! I have also the same problem. Someone fixed...

I have also the same problem. Someone fixed this error?

Forum: De novo discovery 11-30-2011, 06:47 AM
Replies: 11
Views: 6,950
Posted By mcastro
Hi, Recently I used this de novo assembly...


Recently I used this de novo assembly approach to build the transcriptome of a non-sequenced eukaryote: velvet/oases with multiple kmer and Trinity. I joined the different transcriptomes in...
Forum: RNA Sequencing 10-22-2011, 10:23 AM
Replies: 1
Views: 1,977
Posted By mcastro
De novo transcriptome assembly and SNP study with redundant PE reads

Hi all,

I just started to work with NGS data and I have lots of questions/problems about this so I decided to ask for some advice.

I want to analyze SNP and indels of an organism without...
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