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Search: Posts Made By: rdeborja
Forum: Bioinformatics 01-22-2015, 01:53 PM
Replies: 7
Views: 1,573
Posted By rdeborja
A quick starting point

Here's a starting point for you. I copied the 23mer you provided 3 times with a slight modification to the first occurrence.

=== script.pl ======

#!/usr/bin/env perl
use Data::Dumper;

my...
Forum: Bioinformatics 06-11-2014, 04:39 AM
Replies: 3
Views: 3,390
Posted By rdeborja
Thanks for the info. No clue why I didn't see...

Thanks for the info. No clue why I didn't see that in the first place. After confirming the left most and right most reads, the orientation of F2R1 as properly paired clicked in. Thanks again!
Forum: Bioinformatics 06-10-2014, 04:50 AM
Replies: 3
Views: 3,390
Posted By rdeborja
BWA: paired end reads, wrong orientation but listed as properly paired

I have a set of BAM files for a targeted sequencing experiment. After reviewing things in IGV, I noticed that a pair of reads listed as orientation F2R1 are labelled as properly paired. I also...
Forum: Bioinformatics 06-27-2013, 05:51 PM
Replies: 8
Views: 1,961
Posted By rdeborja
I'm a huge fan of makefiles as a very basic...

I'm a huge fan of makefiles as a very basic workflow system, especially since it works well with sge's qmake.
Forum: Bioinformatics 06-26-2013, 04:27 AM
Replies: 8
Views: 1,961
Posted By rdeborja
Data Pipeline Automation, what are you using?

I'm curious to know what type of pipeline workflow automation tool people are using these days. At the start of my career, I started cobbling together various shell scripts which quickly turned into...
Forum: Bioinformatics 01-25-2013, 04:52 AM
Replies: 3
Views: 1,345
Posted By rdeborja
Thanks, didnt catch the thread during my search. ...

Thanks, didnt catch the thread during my search. Much appreciated!
Forum: Bioinformatics 01-22-2013, 11:50 AM
Replies: 3
Views: 1,345
Posted By rdeborja
Varscan header doesn't match the number of columns in the data

I'm using Varscan 2.3.3 with the somatic sub program and noticed the column names (there are 19 based on the output file) but there are 23 columns worth of data below the header. I looked at the...
Forum: Bioinformatics 01-05-2013, 03:34 PM
Replies: 8
Views: 5,190
Posted By rdeborja
Yes, 99.93% read mapping, although it doesn't...

Yes, 99.93% read mapping, although it doesn't include the quality of the mapping. You'll have to look that up in the BAM file independently.
Forum: Bioinformatics 01-05-2013, 09:46 AM
Replies: 8
Views: 5,190
Posted By rdeborja
It generates a summary of reads based on the SAM...

It generates a summary of reads based on the SAM FLAG in column 2 of the BAM file:

4255310402 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
4252238423 + 0 mapped...
Forum: Bioinformatics 01-05-2013, 03:44 AM
Replies: 8
Views: 5,190
Posted By rdeborja
Try using samtools flagstat.

Try using samtools flagstat.
Forum: General 02-01-2012, 07:42 AM
Replies: 4
Views: 1,725
Posted By rdeborja
Staph Aureus and Rhodobacter

Can anyone tell me if staph aureus and rhodobacter are diploid or haploid?
Forum: Bioinformatics 10-18-2011, 09:23 AM
Replies: 9
Views: 15,365
Posted By rdeborja
With BWA output, I usually use Picard's...

With BWA output, I usually use Picard's AddOrRemoveReadGroups.jar before feeding the BAM file to GATK. You can provide all the necessary read group details to ensure GATK works.
Forum: Bioinformatics 07-31-2011, 07:21 PM
Replies: 2
Views: 1,470
Posted By rdeborja
Can you post your ini file for mapping?

Can you post your ini file for mapping?
Forum: Bioinformatics 06-10-2011, 06:12 PM
Replies: 27
Views: 10,837
Posted By rdeborja
Talk about coincidence, I was working on a piece...

Talk about coincidence, I was working on a piece of code that would take Illumina TruSeq export files and merge them into a single bed file just this morning. It outputs only those reads that align...
Forum: Bioinformatics 05-07-2011, 04:25 PM
Replies: 1
Views: 3,550
Posted By rdeborja
Looks like it was a simple solution. Needed to...

Looks like it was a simple solution. Needed to upgrade to the latest version of Samtools (we were using 0.1.12) . Seems like that version of Samtools will use only properly paired reads in the BAM...
Forum: Bioinformatics 05-06-2011, 12:15 PM
Replies: 1
Views: 3,550
Posted By rdeborja
SAMTools showing incorrect depth for a given position

I have a bam file and output from both samtools 0.1.12a and bedtools 2.11.2. The depth provided by samtools pileup is ~4000, samtools mpileup is 592 and bedtools coveragebed 12,995. The bedtools...
Forum: Bioinformatics 02-27-2011, 03:09 PM
Replies: 1
Views: 1,614
Posted By rdeborja
SHRiMP2 for smRNA

I've been working with smRNA data for the last little while trying to come up with a pipeline to replace the AB smRNA tools that we were previously using for SOLiD data. I'm curious to know what...
Forum: Bioinformatics 01-24-2011, 03:28 AM
Replies: 6
Views: 2,815
Posted By rdeborja
BFAST submission to SGE script

Has anyone tried the bfast.submit.pl tool to submit jobs to an SGE cluster? If yes, can you provide an example config script?
Forum: Bioinformatics 01-21-2011, 09:28 AM
Replies: 0
Views: 2,257
Posted By rdeborja
Picard MarkDuplicates throws a java.lang.NegativeArraySizeException

Hi,

I'm running picard's MarkDuplicates on a large .bam file like this:
/jdk1.6.0_10/bin/java -Xmx8g -jar /picard-tools-1.21/MarkDuplicates.jar TMP_DIR=picardTemp INPUT=inFile.bam...
Forum: Bioinformatics 01-04-2011, 08:49 AM
Replies: 6
Views: 1,889
Posted By rdeborja
Has anyone tried aligning to the mature sequences...

Has anyone tried aligning to the mature sequences instead of the entire precursor using BFAST. I've recently jumped on the BFAST bandwagon for genomic data and am trying to find out whether miRNA is...
Forum: SOLiD 12-11-2010, 08:00 PM
Replies: 5
Views: 5,838
Posted By rdeborja
miRNA * non* forms and hairpin

I've been working with the SOLiD smRNA pipeline and have been questioning the genome alignment portion.

I've been using Bioscope to directly align the smRNA reads to the whole genome as 1x36...
Forum: Bioinformatics 12-09-2010, 02:26 PM
Replies: 1
Views: 1,085
Posted By rdeborja
IRC channels

Does anyone know of any good IRC channels to discuss bioinformatics? I noticed #bioperl and received a tweet about #bioruby from @mza.
Forum: Bioinformatics 12-09-2010, 02:28 AM
Replies: 5
Views: 2,282
Posted By rdeborja
Thanks for the tip Kevin. I ended up making a...

Thanks for the tip Kevin. I ended up making a change to our grid engine (implemented consumables for memory and expanded a queue the number of nodes being used) and all is fine. I'm quite impressed...
Forum: Bioinformatics 11-29-2010, 06:38 PM
Replies: 5
Views: 2,282
Posted By rdeborja
Thanks for the advice. I've implemented the...

Thanks for the advice. I've implemented the change as per your recommendation. Unfortunately it didn't resolve my issue. I'm digging into the logs and can hopefully provide an update here to help...
Forum: Bioinformatics 11-28-2010, 05:46 PM
Replies: 5
Views: 2,282
Posted By rdeborja
Bioscope 1.3 Error, suggestions anyone?

I've installed and am currently running the latest version of Bioscope (v1.3) on some test data set. All the demos that accompanied Bioscope 1.3 worked flawlessly but running one of our standard...
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