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Search: Posts Made By: ronton
Forum: Bioinformatics 02-13-2015, 01:13 PM
Replies: 8
Views: 2,436
Posted By ronton
This is why large samples are important in...

This is why large samples are important in genomics. 1000 genomes for example. Each person's genome has variability compared to the next, not necessarily pathogenic or disease-related variants, just...
Forum: Bioinformatics 02-05-2015, 02:22 PM
Replies: 13
Views: 4,190
Posted By ronton
Some people may just use PuTTY or ssh to do data...

Some people may just use PuTTY or ssh to do data analysis on a remote machine/computing cluster.
Forum: Bioinformatics 02-05-2015, 02:19 PM
Replies: 13
Views: 4,190
Posted By ronton
You may want to make a partition and dual boot...

You may want to make a partition and dual boot Linux to save the hassle, unless you only need to perform a small set of specific operations.

Forgive me if you are more experienced with...
Forum: Bioinformatics 11-24-2014, 04:26 PM
Replies: 1
Views: 1,960
Posted By ronton
https://tcga-data.nci.nih.gov/tcga/tcgaDataType.js...

https://tcga-data.nci.nih.gov/tcga/tcgaDataType.jsp
Forum: Bioinformatics 11-05-2014, 10:52 AM
Replies: 9
Views: 2,577
Posted By ronton
Interpreting sequencing data is like a huge...

Interpreting sequencing data is like a huge statistics problem and I would say that several correction steps are often employed such as 'rewarding,' 'penalizing,' etc.

Hopefully others have more...
Forum: Bioinformatics 10-29-2014, 12:41 PM
Replies: 3
Views: 1,414
Posted By ronton
Installing bioinformatics software basic help (set path?)

I have a general question regarding dealing with bioinformatics software.

Many tools seem to have dependencies, for example in order for x to work, you must install samtools first.

For several...
Forum: Bioinformatics 10-15-2014, 03:18 PM
Replies: 2
Views: 2,903
Posted By ronton
I tried vcf-isec and it did not seem to work. ...

I tried vcf-isec and it did not seem to work.

I was eventually able to install and setup vcftools, including sorting, indexing, and compressing the vcf files with tabix and bgzip.

The vcf-isec...
Forum: Bioinformatics 10-10-2014, 02:29 PM
Replies: 2
Views: 2,903
Posted By ronton
How to view only the variants that are present in multiple VCF files?

Suppose I have 10 .vcf files and I want to generate a .vcf file that only contains the common variants that are present in all of the 10 files. Can I use GATK CombineVariants followed by...
Forum: Bioinformatics 09-03-2014, 01:12 PM
Replies: 366
Views: 199,620
Posted By ronton
You're the man! Thank you so much. The command...

You're the man! Thank you so much. The command line and --threads 8 really helps for running multiple samples and so much faster both in setup and run time than clicking through with the interactive...
Forum: Bioinformatics 08-26-2014, 10:43 AM
Replies: 22
Views: 4,916
Posted By ronton
Norbert, I will try to offer my somewhat...

Norbert,

I will try to offer my somewhat informed opinion on this. Of what 'pre-packaged' commercial solutions there might be for bioinformatics analysis, they can be somewhat lacking and/or...
Forum: Bioinformatics 08-21-2014, 02:25 PM
Replies: 12
Views: 7,780
Posted By ronton
Thank you so much for all of your help Brian. I...

Thank you so much for all of your help Brian. I am wondring this too, if preprocessing is something that is necessary and/or how much of a difference it will make. Hopefully I can compare the two...
Forum: Bioinformatics 08-21-2014, 10:18 AM
Replies: 12
Views: 7,780
Posted By ronton
This is a human sample, normal tissue to be...

This is a human sample, normal tissue to be compared with tumor, I figure why not start right with the easy stuff =)

We have a pipeline that we use, but I want to try going through the analysis to...
Forum: Bioinformatics 08-20-2014, 11:41 AM
Replies: 39
Views: 4,194
Posted By ronton
That is actually one of the nice things about...

That is actually one of the nice things about Macs, they are bioinformatics software friendly. You can use Linux on a PC since Windows doesn't run a lot of the software, but with Mac OS can you can...
Forum: Bioinformatics 08-20-2014, 10:39 AM
Replies: 12
Views: 7,780
Posted By ronton
I tried a few step wise passes with BBDuk as a...

I tried a few step wise passes with BBDuk as a kind of experiment and it seems to be a definite improvement.

The original FastQC report for my sample:

http://i.imgur.com/o13cQ9El.png...
Forum: Bioinformatics 08-19-2014, 11:14 AM
Replies: 3
Views: 1,306
Posted By ronton
This is perfect, thank you. The goal is for...

This is perfect, thank you. The goal is for adapter/contaminant trimming/removal. I am a newbie working my way through sequence analysis.
Forum: Bioinformatics 08-19-2014, 09:56 AM
Replies: 3
Views: 1,306
Posted By ronton
How to get sequences of Illumina sequencing reagents/spike ins?

Forgive my ignorance, I am not sure if this is a 'real thing' or if it is of any importance.

I have the sequences of the indexed adapters we use as well as the PCR primers/oligos for library...
Forum: Bioinformatics 08-19-2014, 06:51 AM
Replies: 14
Views: 4,055
Posted By ronton
I've seen this suggestion before; where to find...

I've seen this suggestion before; where to find or how to generate such a file?
Forum: Bioinformatics 08-18-2014, 12:19 PM
Replies: 9
Views: 4,211
Posted By ronton
Perhaps I used the wildcard, I will double check,...

Perhaps I used the wildcard, I will double check, thank you.
Forum: Bioinformatics 08-18-2014, 12:13 PM
Replies: 366
Views: 199,620
Posted By ronton
I tried chmod 755 fastqc (and using sudo before...

I tried chmod 755 fastqc (and using sudo before it) and I get the same result.

'which fastqc' does not return anything, with or without sudo before.

echo $PATH returns
...
Forum: Bioinformatics 08-18-2014, 11:46 AM
Replies: 9
Views: 4,211
Posted By ronton
In addition to what others have stated, there is...

In addition to what others have stated, there is an arguement for not merging the files first, namely parallel computing. Each 'core' can process each smaller file in whichever way you wish, to be...
Forum: Bioinformatics 08-15-2014, 01:05 PM
Replies: 12
Views: 7,780
Posted By ronton
The data we receive is actually several .fastq.gz...

The data we receive is actually several .fastq.gz files per sample, FastQC calls this Casava. As in, several .fastq.gz files that are 'left' for the pair, and matching 'right' .fastq.gz files, per...
Forum: Bioinformatics 08-15-2014, 12:57 PM
Replies: 366
Views: 199,620
Posted By ronton
Those did not seem to work, I don't know. The...

Those did not seem to work, I don't know. The script fastqc is a perl script that runs the java command.

I did put in a bug tracker request to update apt-get.
Forum: Bioinformatics 08-15-2014, 11:35 AM
Replies: 366
Views: 199,620
Posted By ronton
I used sudo apt-get remove fastqc to uninstall...

I used sudo apt-get remove fastqc to uninstall the older version, and then used the commands above to create a link within /usr/local/bin to the /FastQC directory. This works.

However, when I...
Forum: Bioinformatics 08-15-2014, 11:21 AM
Replies: 12
Views: 7,780
Posted By ronton
I guess I should try to rephrase my question....

I guess I should try to rephrase my question. Filtering out and/or trimming as much as possible that is not sample DNA would be a logical first step with the files from the sequencer, wouldn't it?
...
Forum: Bioinformatics 08-14-2014, 11:00 AM
Replies: 12
Views: 7,780
Posted By ronton
Best adapter trimming?

To my understanding, only one sided adapter trimming is necessary as these are the unbound floating ends read in the flow cell.

I would like to trim the adapters from the reads as a first step. I...
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