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Search: Posts Made By: skbrimer
Forum: Bioinformatics 12-15-2016, 07:46 AM
Replies: 4
Views: 1,810
Posted By skbrimer
I'm not sure if grep does duplicates so I don't...

I'm not sure if grep does duplicates so I don't know how to do it in grep. However if you do this it will work:

sort pattern_file > pattern_file_sorted
sort file_a > file_a_sorted
join...
Forum: Bioinformatics 12-14-2016, 09:55 AM
Replies: 678
Views: 202,181
Posted By skbrimer
Thanks for the input guys! I will start playing...

Thanks for the input guys! I will start playing with the updated BBmap as well!
Forum: Bioinformatics 12-14-2016, 08:37 AM
Replies: 678
Views: 202,181
Posted By skbrimer
Thank you Brain! Is there a variant calling...

Thank you Brain!

Is there a variant calling pipeline that works best with BBmap?
Forum: Bioinformatics 12-14-2016, 06:09 AM
Replies: 4
Views: 1,810
Posted By skbrimer
you can use the join command, below is a quick...

you can use the join command, below is a quick tutorial

https://shapeshed.com/unix-join/
Forum: Bioinformatics 12-14-2016, 05:21 AM
Replies: 678
Views: 202,181
Posted By skbrimer
Hi Brian, I like to use freebayes for the...

Hi Brian,

I like to use freebayes for the vcf creation because all of our stuff is haploid, however I do not know how to work with the ref file that BBMap makes during a mapping. Freebayes...
Forum: Ion Torrent 11-14-2016, 01:20 PM
Replies: 1
Views: 3,367
Posted By skbrimer
Hi rsato, Yes it has been released and I...

Hi rsato,

Yes it has been released and I have played with it on a few control libraries. It performs well and the read lengths are 500+ like they promised. They now have a 600bp kit if you have...
Forum: Bioinformatics 03-11-2016, 06:31 AM
Replies: 678
Views: 202,181
Posted By skbrimer
Hi Brian, Thanks for the input, I'm glad to...

Hi Brian,

Thanks for the input, I'm glad to hear that I was interpreting the outputs correctly as a biologist and not a computer engineer. I agree with our interpretation of the results as well....
Forum: Bioinformatics 03-09-2016, 06:47 PM
Replies: 678
Views: 202,181
Posted By skbrimer
Hi Brian, I have been playing with BBmap to...

Hi Brian,

I have been playing with BBmap to see if there is any difference between mapping virus cDNA (RNAseq) with a splice aware aligner vs the default TMAP (Ion Torrent) and I was hoping you...
Forum: Sample Prep / Library Generation 02-02-2016, 06:07 AM
Replies: 2
Views: 1,729
Posted By skbrimer
Smile Thank you lorendarith, These links are...

Thank you lorendarith,

These links are helpful and will give me a narrow window to try :)
Forum: Sample Prep / Library Generation 02-01-2016, 06:10 AM
Replies: 2
Views: 1,729
Posted By skbrimer
Sample input vs genome length or both?

Hellos group,

I have a technical question, I'm working with a viral (surprise!) genome. It is approx 200kbp in length and is a DNA virus. We will be sequencing this on the Ion PGM and I have a...
Forum: Ion Torrent 01-19-2016, 08:31 AM
Replies: 16
Views: 4,244
Posted By skbrimer
Hi carolW, I am not sure how to help you...

Hi carolW, I am not sure how to help you anymore, you have run out of my experience but I do have a few suggestions.

1.) if you have acess (you or someone) to the torrent server hg19 is already...
Forum: Ion Torrent 01-19-2016, 05:51 AM
Replies: 16
Views: 4,244
Posted By skbrimer
I'm not sure about human work since I do...

I'm not sure about human work since I do microbiology, but I thnk @GenoMax may be on the right track. I know that tmap can make the index, here is the techinacl note from Ion...
Forum: Ion Torrent 01-19-2016, 05:35 AM
Replies: 16
Views: 4,244
Posted By skbrimer
you should be fine, its just saying it found an...

you should be fine, its just saying it found an ambigous base pair and is fixing it. If you look in the folder with your referance if it worked, there should be a ".tmap.anno", "tmap.bwt",...
Forum: Ion Torrent 01-18-2016, 06:43 AM
Replies: 16
Views: 4,244
Posted By skbrimer
no problems, I think I see what you are doing...

no problems, I think I see what you are doing wrong because it is what I did wrong, Did you go to github and clone(download) only the TMAP subdirectory?
Forum: Ion Torrent 01-18-2016, 06:10 AM
Replies: 16
Views: 4,244
Posted By skbrimer
Smile sorry I didn't answer this question as well. The...

sorry I didn't answer this question as well. The library you are wanting is the boost library. Its in the list for the BUILD file.

Good Luck
Forum: Ion Torrent 01-18-2016, 06:02 AM
Replies: 16
Views: 4,244
Posted By skbrimer
Okay, I'm going to assume you are using Ubuntu...

Okay, I'm going to assume you are using Ubuntu for this so cut and paste the following in your terminal window.

apt-get update

apt-get install \
build-essential \
...
Forum: Ion Torrent 01-18-2016, 05:52 AM
Replies: 16
Views: 4,244
Posted By skbrimer
Hi Carol, There is not a bug and you are...

Hi Carol,
There is not a bug and you are missing an external library dependency "zlib1g-dev" if you install that library and redo the build script it should work just fine.
Sean
Forum: Bioinformatics 01-13-2016, 07:16 AM
Replies: 8
Views: 2,152
Posted By skbrimer
Hi everyone! Thank you for the input, I am using...

Hi everyone! Thank you for the input, I am using TMAP(modified BWA) and BWA. So I have not used bowtie 2 before but it is a splice aware mapper correct? So I have 2 votes for using a splice aware vs...
Forum: Bioinformatics 01-11-2016, 11:44 AM
Replies: 8
Views: 2,152
Posted By skbrimer
Split N Trim RNAseq data

Hello everyone,

I have more of a general pre-processing question. We are doing some small viral genome sequencing. The virus is ssRNA (coronaviridae) and we have been using the RNAseq method on...
Forum: Ion Torrent 11-16-2015, 12:50 PM
Replies: 5
Views: 3,018
Posted By skbrimer
Sooo... how does one evaluate an error rate with...

Sooo... how does one evaluate an error rate with a reference? Is it just a comparison of the vcf files?

Also why would it be bad to error correct in those situations, I imagine that it will have...
Forum: Ion Torrent 11-16-2015, 12:26 PM
Replies: 5
Views: 3,018
Posted By skbrimer
Thanks Brian :) Are there time when you...

Thanks Brian :)

Are there time when you would not want to error correct?
Forum: Ion Torrent 11-16-2015, 11:09 AM
Replies: 5
Views: 3,018
Posted By skbrimer
Post Ion torrent error correction

I asked this question on the Ion Community a couple of months ago without an answer or reply so I thought I would try here.

Over the last several years Ion Torrent has improved it chemistry and...
Forum: Ion Torrent 11-16-2015, 11:00 AM
Replies: 1
Views: 3,741
Posted By skbrimer
Your data looks pretty normal for Ion Torrent. I...

Your data looks pretty normal for Ion Torrent. I do not use proton data since I'm in the low throughput microbe world. There are a couple of things going on here in your question.

First, your...
Forum: Bioinformatics 07-13-2015, 06:42 AM
Replies: 0
Views: 814
Posted By skbrimer
Samtools mpileup help, version 1.2

Good morning group,

I have a quick question about how mpileup and bcftools consensus work with segmented genomes. Right now I have genome with 10 segments as the reference file and when I try to...
Forum: Bioinformatics 06-30-2015, 05:23 AM
Replies: 0
Views: 939
Posted By skbrimer
Standalone TMAP 3.4.1 error

Good Morning gang,

I have had, for the first time TMAP fail to put together some PGM reads for me. I do not blame the algorithm the data is not the best, but it is weird.

Below is the code I...
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