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Forum: Bioinformatics 07-17-2015, 06:06 AM
Replies: 0
Views: 1,828
Posted By trotos
Yet Another bwa mem unique post

So, I am using the following version of BWA

Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.7.12-r1039</pre>

I got through a lot threads read answers and so on... still...
Forum: Bioinformatics 07-15-2015, 06:54 AM
Replies: 5
Views: 13,160
Posted By trotos
hello, I dig up this post because of your comment...

hello, I dig up this post because of your comment on the SA: tag
could you please elaborate, the provided link is broken.
the main question is:
are the reads with the SA: code still unique? what...
Forum: Bioinformatics 11-21-2014, 04:20 AM
Replies: 7
Views: 2,293
Posted By trotos
still the same i'm providing a little bit of...

still the same
i'm providing a little bit of the error messages:
PROGRAM_RECORD_ID=MarkDuplicates
PROGRAM_GROUP_NAME=MarkDuplicates
MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000...
Forum: Bioinformatics 11-21-2014, 04:15 AM
Replies: 7
Views: 2,293
Posted By trotos
thank you for the answer,

thank you for the answer,
Forum: Bioinformatics 11-21-2014, 03:54 AM
Replies: 7
Views: 2,293
Posted By trotos
As I got the same error, I also would like to...

As I got the same error, I also would like to know the answer to that, because sometimes if it works the best way to do go is not to play arround.
So if anyone knows about JDK could please provide...
Forum: Bioinformatics 08-11-2014, 02:09 AM
Replies: 62
Views: 27,958
Posted By trotos
recomended command for paired ends

Hi, replimoc

I'm realy new to all this staff so I would like a guide. I did an MNase-seq experiment I got paired end reads and I got the following fastqc results:

with per base sequence...
Forum: Bioinformatics 05-19-2014, 07:35 AM
Replies: 5
Views: 4,775
Posted By trotos
Is there any way to annotate the enchancers??? ...

Is there any way to annotate the enchancers???
I will really need this answer.
Forum: Bioinformatics 05-19-2014, 07:33 AM
Replies: 5
Views: 4,775
Posted By trotos
I fixed this one, I needed to enter something...

I fixed this one, I needed to enter something like the following to the very end of ~/.bashrc and only there. anything else didn't work or the system failed to login.
Forum: Bioinformatics 05-19-2014, 07:29 AM
Replies: 1
Views: 793
Posted By trotos
after piccard MarkDuplicates drop in mapping percentage

java -Xmx14g -jar MarkDuplicates.jar INPUT=file.sorted.bam OUTPUT=file.noDUP.bam REMOVE_DUPLICATES=TRUE METRICS_FILE=metrics2.log
I'me running the above command.
Flagstat on the sorted bam is,...
Forum: Bioinformatics 05-06-2014, 11:44 PM
Replies: 5
Views: 4,775
Posted By trotos
ngsplot errors and questions

I tried to find any similar questions but I couldn't

So, I'm under ubuntu 14.04 64bit 32GB memmory

First
is the installation of ngsplot, I followed the guide as it is described...
Forum: Bioinformatics 06-29-2013, 08:32 AM
Replies: 0
Views: 792
Posted By trotos
build a web service for database access

Dear all

I do not know if there has been any guides or threads already with answers, but my search couldn't find any.
I'm looking for a guideline in to build and maintain a web server, in which...
Forum: Introductions 05-27-2013, 09:22 AM
Replies: 0
Views: 669
Posted By trotos
Hello

Just a simple hello from me hope to learn a lot for next-gen from this site
Be good
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