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Search: Posts Made By: JMFA
Forum: Bioinformatics 02-25-2015, 05:25 AM
Replies: 4
Views: 1,704
Posted By JMFA
This is actually 100bp PE DNAseq data. I've...

This is actually 100bp PE DNAseq data.
I've clipped the adapter sequences and the Kmer profile looks much better (not perfect but better)!...
Forum: Bioinformatics 02-24-2015, 05:01 AM
Replies: 4
Views: 1,704
Posted By JMFA
Hi! Thanks for the reply :) Yes. Running...

Hi!
Thanks for the reply :)

Yes. Running w/out the "--casava" option was the first thing that I did. However, I got some weird Kmer profiles. FASTQC doesn't detect any adapter content /...
Forum: Bioinformatics 02-24-2015, 12:27 AM
Replies: 4
Views: 1,704
Posted By JMFA
Casava FASTQ from SRA

Dear all,

I am currently trying to perform quality checks on a set of FASTQ files (downloaded from SRA) that (according to the authors) were generated using CASAVA 1.8.1 pipeline.

Since all...
Forum: Bioinformatics 01-31-2013, 08:06 AM
Replies: 6
Views: 7,710
Posted By JMFA
Dear all, thank you very much for the comments!...

Dear all,
thank you very much for the comments!

I decided to upgrade the OS to 64-bit!
Forum: Bioinformatics 01-30-2013, 02:44 AM
Replies: 6
Views: 7,710
Posted By JMFA
dear xied75, Thanks for the reply! No. I'm...

dear xied75,

Thanks for the reply!
No. I'm running a 32-bit version of ubuntu 12.04.1 LTS

file bwa gives this output
Forum: Bioinformatics 01-29-2013, 05:15 AM
Replies: 6
Views: 7,710
Posted By JMFA
BWA index segmentation fault

Dear all,

I'm having some difficulties trying to index a reference genome using BWA -a bwtsw.
I am using BWA 0.6.2 version and I tried to index the Hg19 but BWA fails to complete the index.
...
Forum: Bioinformatics 01-11-2013, 02:42 AM
Replies: 2
Views: 1,700
Posted By JMFA
Dear cwhelan, Thanks for the reply! Yes!...

Dear cwhelan,

Thanks for the reply!
Yes! Maybe its normal because I only get a few strange peaks.

Thanks again,
J
Forum: Bioinformatics 01-10-2013, 02:56 AM
Replies: 2
Views: 1,700
Posted By JMFA
Extremely high Coverage in some regions

Dear all,

I am currently working with NGS data for one individual sequenced using Illumina HiSeq 2000 (13-16x coverage).
I follow some standard pipelines to align and prepare the data for variant...
Forum: Bioinformatics 12-02-2010, 08:26 AM
Replies: 0
Views: 2,111
Posted By JMFA
Unhappy New Tools to analyze Next Gen Seq data

Dear all,

I'm currently using GATK and Samtools to analyze some NGS data from the 1000genomes project.

However I'm having some difficulties in understanding what I can do with the recalibrated...
Forum: Bioinformatics 11-25-2010, 05:06 AM
Replies: 2
Views: 3,587
Posted By JMFA
Thanks, Sven! That worked perfectly! ...

Thanks, Sven!

That worked perfectly!

Cheers,
Joao
Forum: Bioinformatics 11-24-2010, 01:24 AM
Replies: 2
Views: 3,587
Posted By JMFA
Question Tabix Error on Ubuntu 10.04

Dear all,

I'm having problems installing Tabix on Ubuntu 10.04.
Samtools is already installed and working properly. I downloaded the tabix bz2 file from the sourceforge webpage, extracted all the...
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