SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 38
Search took 0.03 seconds.
Search: Posts Made By: simobioinfo
Forum: Genomic Resequencing 01-18-2016, 07:30 AM
Replies: 5
Views: 6,073
Posted By simobioinfo
Hi, I'm working with targeted Ion torrent PGM...

Hi,
I'm working with targeted Ion torrent PGM data, that is a small panel of genes.
I would like to know if there are methods to identify CNVs from such a kind of data.
Thank you in advance
Forum: Bioinformatics 01-18-2016, 07:20 AM
Replies: 8
Views: 3,020
Posted By simobioinfo
Hi, I'm working with targeted Ion torrent PGM...

Hi,
I'm working with targeted Ion torrent PGM data.
I would like to know if there are methods to identify CNVs from such a kind of data.
Thank you in advance
Forum: Ion Torrent 11-20-2015, 02:18 AM
Replies: 5
Views: 9,093
Posted By simobioinfo
Hi, anyone tried to analyze simulated data with...

Hi,
anyone tried to analyze simulated data with torrent suite installed on a personal server?
Forum: Bioinformatics 09-25-2015, 05:26 AM
Replies: 25
Views: 18,367
Posted By simobioinfo
Hi, I would like to install CNVnator. I...

Hi,
I would like to install CNVnator. I installed root and setted environmental variable.
In detail, the directory where i decompressed root is /root/source-codes/root and to set environmental...
Forum: RNA Sequencing 09-22-2015, 01:39 AM
Replies: 15
Views: 8,942
Posted By simobioinfo
Because the experiment is performed as paired end

Because the experiment is performed as paired end
Forum: RNA Sequencing 09-22-2015, 01:32 AM
Replies: 15
Views: 8,942
Posted By simobioinfo
Then I have to separate my fastq files into two...

Then I have to separate my fastq files into two files... and how?
Forum: RNA Sequencing 09-22-2015, 12:40 AM
Replies: 15
Views: 8,942
Posted By simobioinfo
The data are paired for sure. I ran bwa mem ...

The data are paired for sure.
I ran bwa mem
bwa mem ../../hg19.fa Campione_2.fastq > Campione_2.sam
Then through
samtools view -bS campione_2.sam > campione_2.bam
and then samtools flagstat....
Forum: RNA Sequencing 09-16-2015, 06:10 AM
Replies: 15
Views: 8,942
Posted By simobioinfo
Hi, I aligned through bwa mem fastq files...

Hi,
I aligned through bwa mem fastq files generated from ion torrent pgm in order to analyze data with breakdancer to detect structural variants.
However samtools flagstat gives these results:...
Forum: Bioinformatics 09-09-2015, 05:37 AM
Replies: 26
Views: 12,664
Posted By simobioinfo
Hi, I'm trying to analyze with breakdancer data...

Hi,
I'm trying to analyze with breakdancer data coming from ion torrent, which were aligned through tmap.
I ran bam2cfg.pl but I obtained an empty file.
This is the message:
[Wed Sep 9 15:26:19...
Forum: Bioinformatics 08-11-2015, 11:05 PM
Replies: 13
Views: 2,377
Posted By simobioinfo
and finally I got it... I installed samtools...

and finally I got it... I installed samtools independently from breakdancer installation.
Then I modified the cmakefile eliminating the part regarding samtools installation and so I solved my...
Forum: Bioinformatics 08-10-2015, 06:27 AM
Replies: 13
Views: 2,377
Posted By simobioinfo
I'm working with ubuntu. I restart from the...

I'm working with ubuntu.
I restart from the beginning.
I tried to install samtools but I failed.
I tried to put the tar.bz2 file into the vendor directory changing extension in tar.gz and launched...
Forum: Bioinformatics 08-10-2015, 04:40 AM
Replies: 13
Views: 2,377
Posted By simobioinfo
in the /root/breakdancer/build/vendor/ directory...

in the /root/breakdancer/build/vendor/ directory I found a directory named samtools.
Do I have to remove it before to install samtools?
Forum: Bioinformatics 08-10-2015, 04:15 AM
Replies: 13
Views: 2,377
Posted By simobioinfo
So if understand you suggest me to: -download...

So if understand you suggest me to:
-download samtools
-to put the tar.bz2 file into /root/breakdancer/build/vendor/ directory
and then?
Do I have to install it into that directory?
If yes....
Forum: Bioinformatics 08-10-2015, 02:50 AM
Replies: 13
Views: 2,377
Posted By simobioinfo
Hi, I read documentation and the message error...

Hi,
I read documentation and the message error was:
[ 10%] Performing build step for 'boost-libs'
[ 12%] No install step for 'boost-libs'
[ 14%] Completed 'boost-libs'
[ 14%] Built target...
Forum: Bioinformatics 08-04-2015, 02:35 AM
Replies: 13
Views: 2,377
Posted By simobioinfo
Hi, I have problems in installing breakdancer. ...

Hi,
I have problems in installing breakdancer.
I downloaded the zip file from sourceforce and decompressed it.
I found two suddirectories, perl and cpp.
I try to make in cpp directory but I'm not...
Forum: Bioinformatics 08-04-2015, 01:38 AM
Replies: 5
Views: 2,865
Posted By simobioinfo
Hi, I have problems in installing breakdancer. ...

Hi,
I have problems in installing breakdancer.
I downloaded the zip file from sourceforce and decompressed it.
I found two suddirectories, perl and cpp.
I try to make in cpp directory but I'm not...
Forum: Bioinformatics 09-17-2014, 05:25 AM
Replies: 39
Views: 3,166
Posted By simobioinfo
Thank you everybody. I was on vacation. I will...

Thank you everybody. I was on vacation. I will try soon indexes you sent me
Forum: Bioinformatics 08-23-2014, 10:54 PM
Replies: 39
Views: 3,166
Posted By simobioinfo
My mac has 4Gb of RAM. I suppose that it could be...

My mac has 4Gb of RAM. I suppose that it could be enough to build index. I don't know how to check ram usage.
Forum: Bioinformatics 08-23-2014, 01:11 AM
Replies: 39
Views: 3,166
Posted By simobioinfo
Hi... now 24 hours are passed and indexing is...

Hi... now 24 hours are passed and indexing is still running on my MAc (see previous post of this thread). What can I do now? My processor is dual core... I have to insert an option into the command...
Forum: Bioinformatics 08-22-2014, 02:36 AM
Replies: 39
Views: 3,166
Posted By simobioinfo
Thank you. Indexing is started now. I have 4...

Thank you. Indexing is started now. I have 4 files:
3.bt2 of 4kb
4.bt2 of 716.2 Mb
1.bt2 and 2.bt2 are 0 byte at the moment.
Is that ok?
Forum: Bioinformatics 08-22-2014, 01:06 AM
Replies: 39
Views: 3,166
Posted By simobioinfo
I will try...

I will try...
Forum: Bioinformatics 08-22-2014, 12:34 AM
Replies: 39
Views: 3,166
Posted By simobioinfo
Hi again... first of all I would like to thank...

Hi again... first of all I would like to thank you everybody.
Yesterday I tried to index human genome on my Mac with this command:
bowtie2-build * genome.fa>genome
Shell has been showing me this...
Forum: Bioinformatics 08-20-2014, 11:38 AM
Replies: 39
Views: 3,166
Posted By simobioinfo
Thank you Genomax! Now you encouraged me!

Thank you Genomax! Now you encouraged me!
Forum: Bioinformatics 08-20-2014, 11:09 AM
Replies: 39
Views: 3,166
Posted By simobioinfo
Biocomputer: I'm using VM because a Windows PC is...

Biocomputer: I'm using VM because a Windows PC is available and I don't know how to use bowtie in windows because I use it from command line. I have a question 1.5Gb is enough to run alignments?...
Forum: Bioinformatics 08-20-2014, 10:47 AM
Replies: 39
Views: 3,166
Posted By simobioinfo
I would like to use institutional resources but I...

I would like to use institutional resources but I have been wait for a new PC for 2 years (in Italy research is very difficult) and now I have to start my work. So I think that using my Mac could be...
Showing results 1 to 25 of 38

 


All times are GMT -8. The time now is 01:01 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO