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Forum: Core Facilities 09-20-2018, 06:24 PM
Replies: 1
Views: 4,937
Posted By ramirob
Organizing projects, data inputs and output

Hello!

Do you have any suggestions, pointers, references, models on how to organize projects and their correspondingraw data, rmarkdowns, results, etc?

We do a lot of bioinformatics projects,...
Forum: Bioinformatics 03-19-2013, 08:08 AM
Replies: 3
Views: 2,603
Posted By ramirob
Adaptor removal, trimming, vs masking

I had a question about best practices regarding adaptor removing, trimming the ends of reads, and also removing short reads. All of these questions pertain preparing sequences for alignment with...
Forum: Bioinformatics 02-15-2013, 08:58 AM
Replies: 4
Views: 1,416
Posted By ramirob
Thnaks Richard! We are talking about huge...

Thnaks Richard!

We are talking about huge genome alignments. The samples have already been aligned to reference (this was part of an NGS experiment). My understanding is that bl2seq is more for...
Forum: Bioinformatics 02-15-2013, 08:48 AM
Replies: 4
Views: 1,416
Posted By ramirob
Comparing sequences between themselves

Hello,

We ran an experiment where we sequenced WT and mutant isolates from the same particular organism. We have aligned these samples to reference (using BWA) and then found SNPs (using GATK)....
Forum: Bioinformatics 07-17-2012, 02:19 PM
Replies: 5
Views: 2,223
Posted By ramirob
Not really, but if I filter the gatk output I...

Not really, but if I filter the gatk output I would just get less variants wouldn't I? The main question I have is, are the parameters I am using ok? Maybe I can check other alignments. I have...
Forum: Bioinformatics 07-17-2012, 05:50 AM
Replies: 5
Views: 2,223
Posted By ramirob
Well, with vcf-compare I am getting about 30%! ...

Well, with vcf-compare I am getting about 30%!

# The command line was: vcf-compare(r731) chr10gatk.raw.vcf.gz chr10.samtools.raw.vcf.gz
#
#VN 'Venn-Diagram Numbers'. Use `grep ^VN | cut -f 2-`...
Forum: Bioinformatics 07-15-2012, 04:40 PM
Replies: 5
Views: 2,223
Posted By ramirob
Little concordance between GATK and Samtools

Hello,

I have read that GATK and Samtools should give you about 90% concordance (Hugeseq test). I am not able to reproduce that and was wondering if anyone has done it and can tell me what...
Forum: Bioinformatics 06-05-2012, 11:42 PM
Replies: 6
Views: 4,677
Posted By ramirob
Hi everyone, In relationship to this, I am...

Hi everyone,

In relationship to this, I am trying to assess concordance as well, but on the contrary, I am getting an overlap of around 30%! (as described by vcf-compare in vcftools). I am not...
Forum: Bioinformatics 06-05-2012, 11:36 PM
Replies: 6
Views: 4,677
Posted By ramirob
Hi everyone, In relationship to this, I am...

Hi everyone,

In relationship to this, I am trying to assess concordance as well, but on the contrary, I am getting an overlap of around 30%! (as described by vcf-compare in vcftools). I am not...
Forum: Bioinformatics 05-22-2012, 03:38 AM
Replies: 9
Views: 2,261
Posted By ramirob
I must admit I just gave up on Casava alignments,...

I must admit I just gave up on Casava alignments, just use BWA and I am exploring other aligners.
Forum: Bioinformatics 04-13-2012, 11:01 AM
Replies: 9
Views: 2,261
Posted By ramirob
sdriscoll, It seems that mpileup looking...

sdriscoll,

It seems that mpileup looking like:

chr1.fa 3309 N 1 ^NT C
chr1.fa 3310 N 1 G C
chr1.fa 3311 N 1 C F
chr1.fa 3312 N 1 C F

is a bad sign, it looks to me that it is not mapping...
Forum: Bioinformatics 04-10-2012, 04:17 PM
Replies: 9
Views: 2,261
Posted By ramirob
Samtools on Chromosomes Versus Genome

Hi everyone,

Does anybody have experience running samtools on CASAVA alignments?

I am trying to call SNPs using samtools on a CASAVA/illumina alignment.

CASAVA outputs an alignment of the...
Forum: Bioinformatics 04-01-2012, 04:28 AM
Replies: 1
Views: 2,940
Posted By ramirob
[sam_read1] reference 'chrN.fa' is recognized as '*'

Hello,

I aligned some human samples with Casava, and then converted the alignments to SAM using samtools:

llumina_export2sam.pl --read1=file_R1.export.txt.gz --read2=file_R2.export.txt.gz >...
Forum: Introductions 04-01-2012, 04:15 AM
Replies: 2
Views: 1,059
Posted By ramirob
Hello from Vermont

Hi everyone,

Just a quick introduction from beautiful Burlington Vermont. I am helping out processing the data from an illumina machine and learning all about running alignments and calling...
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