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Search: Posts Made By: golharam
Forum: Bioinformatics 08-04-2015, 09:51 AM
Replies: 0
Views: 797
Posted By golharam
How to get bwa to report one alignment per read or read pair

I'm using bwa with the parameters 'sampe -n 1 -N 0' to report 1 alignment per read for a paired-end dataset. However, in the output sam file, I see the same forward/reverse pair report twice to...
Forum: General 04-22-2015, 07:15 AM
Replies: 3
Views: 1,462
Posted By golharam
NGS Project / Data Management Software

Hi all - I'm looking for a NGS project and data management system. Basically something that will keep track of projects, users, data, etc. It doesn't need to be specific for NGS, but would help. ...
Forum: Introductions 02-06-2015, 12:35 PM
Replies: 13
Views: 3,017
Posted By golharam
Can you tell me what papers you are referring to?

Can you tell me what papers you are referring to?
Forum: Introductions 02-06-2015, 08:23 AM
Replies: 13
Views: 3,017
Posted By golharam
I don't think its possible to find gene fusions...

I don't think its possible to find gene fusions from DNA exome data. You would need RNA data instead. You can find SNPs with exome data but doubtful you can attribute them to gene fusions unless...
Forum: Illumina/Solexa 01-16-2015, 11:02 AM
Replies: 3
Views: 1,888
Posted By golharam
MiSeq FastQ Header for pair-end data

So the Miseq fastq header for pair-end data has changed. I used to see a /1 or /2 at the end of the read name. Now I get something like this for the first read:

@HWI:1:X:2:1101:1094:2143 1:N:0:...
Forum: General 12-12-2014, 12:42 PM
Replies: 6
Views: 6,571
Posted By golharam
How exactly are you supposed to interpret...

How exactly are you supposed to interpret normalized coverage? For instance, I have a bunch of samples that got sequenced. For 1 specific target the length of the target is approximately 3000bp. ...
Forum: Bioinformatics 11-17-2014, 08:24 AM
Replies: 18
Views: 14,319
Posted By golharam
I get this problem as well using tophat2 aligned...

I get this problem as well using tophat2 aligned BAM files, position sorted. I will revert to name sorting.
Forum: Bioinformatics 10-31-2014, 08:48 AM
Replies: 1
Views: 1,523
Posted By golharam
As far as I'm aware of, yes. The filename is...

As far as I'm aware of, yes. The filename is slightly different, one replace .bam with .bai while the other add .bai to the end of .bam.
Forum: Bioinformatics 10-01-2014, 09:32 AM
Replies: 0
Views: 941
Posted By golharam
Rat (rn5) / GATK Variant Recalibration

Hi all - I'm doing some work with rat (rn5) and am using GATK to recalibration quality scores. GATK's VariantRecalibrator requires a set of high quality SNPs (in VCF format) in order to train its...
Forum: Bioinformatics 12-06-2012, 08:37 AM
Replies: 3
Views: 1,808
Posted By golharam
I last used this: Taslim C, Wu J, Yan P,...

I last used this:

Taslim C, Wu J, Yan P, Singer G, Parvin J, Huang T, Lin S, Huang K. Comparative study on ChIP-seq data: normalization and binding pattern characterization, Bioinformatics, Vol....
Forum: Bioinformatics 11-04-2012, 08:08 PM
Replies: 7
Views: 2,992
Posted By golharam
I see TMAP on...

I see TMAP on github...https://github.com/iontorrent/TMAP

I think I'll try that.
Forum: Bioinformatics 11-04-2012, 08:06 PM
Replies: 7
Views: 2,992
Posted By golharam
Ion Torrent Mappers

Hi all - I'm getting (my first) Ion Torrent data set from a collaborator. It appears I have to use the Torrent Suite application which is only available on the Ion Torrent Cloud or downloaded as a...
Forum: General 09-17-2012, 12:28 PM
Replies: 2
Views: 5,431
Posted By golharam
yes, thank you!

yes, thank you!
Forum: General 09-14-2012, 09:19 AM
Replies: 2
Views: 5,431
Posted By golharam
GTF file from UCSC with Gene name???

Here's a simple question...I have a list of gene names that I want to retrieve a GTF file of those genes specifically. I put the list into UCSC for RefSeq genes and download the GTF file. The...
Forum: Bioinformatics 08-02-2012, 10:33 PM
Replies: 0
Views: 1,040
Posted By golharam
How to merge interval files generated from RealignerTargetCreator

Hi all - I'm using GATK realigner which can take several hours on my human samples. I'm trying to optimize my pipeline by dividing this up by chromosome for each node in my cluster. I can call...
Forum: Bioinformatics 06-28-2012, 08:50 AM
Replies: 7
Views: 5,352
Posted By golharam
EMBOSS has tools available to do this

EMBOSS has tools available to do this
Forum: Bioinformatics 06-19-2012, 01:45 PM
Replies: 32
Views: 35,384
Posted By golharam
I had this problem too. I actually built a sub...

I had this problem too. I actually built a sub sampler that works on fragment and paired-end fastq (gzip'ed or not) data. Its written in Java and based on the Picard framework. ...
Forum: Bioinformatics 06-15-2012, 09:27 AM
Replies: 7
Views: 5,508
Posted By golharam
any change to GATK for this?

I recently came across this problem with GATK 1.4-14-g2e47336. I assume this was changed a long time ago. Tophat still output 255 for mapping quality. Does anyone know if tophat or GATK has...
Forum: Bioinformatics 06-11-2012, 10:12 PM
Replies: 4
Views: 1,972
Posted By golharam
I believe Illumina's Human Body Map data is...

I believe Illumina's Human Body Map data is stranded. Have you tried searching NCBI's SRA?
Forum: Bioinformatics 05-31-2012, 11:42 AM
Replies: 0
Views: 2,237
Posted By golharam
cufflinks XLOC identifiers

Hi all - I'm using tophat/cufflinks/cuffdiff to compare RNA-Seq samples for differential expression. cuffdiff reports in a file the differential expression of cds regions. The id's for each region...
Forum: Bioinformatics 05-23-2012, 09:44 AM
Replies: 5
Views: 3,633
Posted By golharam
Use Tophat. You will need a GTF file of exons,...

Use Tophat. You will need a GTF file of exons, CDS, etc. Tophat will map to the known transcriptome then map to the rest of the genome.
Forum: SOLiD 04-19-2012, 07:58 AM
Replies: 22
Views: 5,987
Posted By golharam
I agree. I only use LifeScope to map data, and I...

I agree. I only use LifeScope to map data, and I use the command-line interface. The GUI is horrible. Once I have the BAM files I do the rest of my processing outside of LifeScope.

I ask...
Forum: Bioinformatics 04-18-2012, 03:41 PM
Replies: 3
Views: 3,716
Posted By golharam
Unfortunately they are all not Java. GATK is...

Unfortunately they are all not Java. GATK is Java, but GATK has some complexities I'm trying to avoid. I'm actually building a version similar to Picard, or at least shares the same infrastructure.
Forum: Bioinformatics 04-18-2012, 01:29 PM
Replies: 3
Views: 3,716
Posted By golharam
Java libaray/API for VCF file

Hi all,

Is there a Java library for VCF files as Picard is for SAM/BAM files?

A quick google search didn't turn anything up.
Forum: SOLiD 04-18-2012, 12:17 PM
Replies: 22
Views: 5,987
Posted By golharam
Just out of curiosity, why are you not using...

Just out of curiosity, why are you not using LifeScope?
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