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Search: Posts Made By: Cytosine
Forum: Bioinformatics 12-04-2014, 09:19 AM
Replies: 5
Views: 3,653
Posted By Cytosine
I tried to help by telling him to use sample...

I tried to help by telling him to use sample files as a guideline... as that is exactly what I have done myself when I started with Circos and I still do every time when I make a new visualization. ...
Forum: Bioinformatics 12-04-2014, 01:03 AM
Replies: 5
Views: 3,653
Posted By Cytosine
Parsing your data into a proper format should be...

Parsing your data into a proper format should be pretty straightforward and you can help yourself with sample files from the website.

If you want an easier way, then you should use an alternative...
Forum: Bioinformatics 09-13-2014, 12:55 AM
Replies: 8
Views: 2,605
Posted By Cytosine
Your tophat compilation went without any...

Your tophat compilation went without any problems? It should notify you at that point if it cannot find samtools.

Try doing a clean reinstall and note any logged warnings or errors being reported...
Forum: Bioinformatics 09-09-2014, 12:29 AM
Replies: 1
Views: 871
Posted By Cytosine
Tried cross referencing the GI's with databases...

Tried cross referencing the GI's with databases like KEGG, Uniprot or Genbank yet?
Forum: Bioinformatics 09-05-2014, 11:56 AM
Replies: 4
Views: 2,511
Posted By Cytosine
Of course, you can do that with Genbank. ...

Of course, you can do that with Genbank.

Perform a query to find all viral sequences and once you get the results, select in the dropdown menu:
- send to
- File
- format FASTA
- create file...
Forum: Bioinformatics 09-05-2014, 07:08 AM
Replies: 4
Views: 2,511
Posted By Cytosine
The most straightforward approach for this is to...

The most straightforward approach for this is to set up a local database for your organism.

As for remote queries on NCBI's servers, well... AFAIK (correct me if I'm wrong) blast+ suite does not...
Forum: RNA Sequencing 08-25-2014, 06:58 AM
Replies: 4
Views: 3,924
Posted By Cytosine
I believe using proteomics approaches to...

I believe using proteomics approaches to indentify secreted proteins is the way to go.

As mbblack said, RNA-Seq will not tell you enough about the protein level in the sample and will give you...
Forum: Bioinformatics 08-20-2014, 12:49 AM
Replies: 5
Views: 3,213
Posted By Cytosine
Hi, 1) I guess it depends on what you want...

Hi,

1) I guess it depends on what you want to achieve. For resequencing runs I would use repeat masking on the genome, for CNV analyses I would not mask the genome.

2) Why mask reads? That...
Forum: Bioinformatics 08-20-2014, 12:35 AM
Replies: 1
Views: 1,325
Posted By Cytosine
I'd say a DBMS and a server-side scripting...

I'd say a DBMS and a server-side scripting language for the back-end and some Javascript/HTML5/CSS3 for the front-end.
Forum: Bioinformatics 08-11-2014, 02:39 AM
Replies: 3
Views: 1,188
Posted By Cytosine
Hard to say... could be that the UCSC sets are...

Hard to say... could be that the UCSC sets are not complete, or maybe a high sequence redundancy between ncRNAs?

I'd recommend SortMeRNA (http://bioinfo.lifl.fr/RNA/sortmerna/) for getting rid of...
Forum: Introductions 08-11-2014, 12:20 AM
Replies: 4
Views: 3,623
Posted By Cytosine
You did compile it successfully. Now you need to...

You did compile it successfully. Now you need to specify the correct path to it if you want to use it.

You can't go wrong with a fullpath name:
...
Forum: Bioinformatics 08-10-2014, 03:16 AM
Replies: 14
Views: 10,372
Posted By Cytosine
you're missing the C++ compiler. If you're...

you're missing the C++ compiler.

If you're on a debian-based distro just do sudo apt-get install g++ and try again.
Forum: Bioinformatics 08-09-2014, 09:48 AM
Replies: 9
Views: 8,633
Posted By Cytosine
Anyone yet tried updating their SQLite and...

Anyone yet tried updating their SQLite and RSQL-DBI?

Seems like the problem is in the database interface.
Forum: Bioinformatics 08-08-2014, 01:31 AM
Replies: 2
Views: 1,936
Posted By Cytosine
You could have a go with R and it's packages for...

You could have a go with R and it's packages for pathway enrichment tests (e.g. GOStats or topGO).

If you have a lot of input files, then scripting such a task like will make your life a lot...
Forum: Bioinformatics 08-04-2014, 11:13 PM
Replies: 3
Views: 3,403
Posted By Cytosine
Please provide sessionInfo() so we can better...

Please provide sessionInfo() so we can better assist you...


dge <- dge[A>10,,keep.lib.sizes=FALSE]
Error in object[[a]][i, , drop = FALSE] : incorrect number of dimensions


I see a double...
Forum: Bioinformatics 08-04-2014, 12:31 AM
Replies: 34
Views: 14,590
Posted By Cytosine
There is an old post about this same problem on...

There is an old post about this same problem on this forum: link (http://seqanswers.com/forums/archive/index.php/t-7391.html)

There it is proposed to rename the functions in the DFLAGS line in the...
Forum: Bioinformatics 08-03-2014, 11:29 PM
Replies: 34
Views: 14,590
Posted By Cytosine
That's odd... The expl and logl function...

That's odd... The expl and logl function declarations are in math.h, which you are including in your makefile.

Did you do make clean after each try? Could be some code got compiled without it and...
Forum: Bioinformatics 08-03-2014, 10:52 PM
Replies: 34
Views: 14,590
Posted By Cytosine
Undefined reference would probably mean you...

Undefined reference would probably mean you unlinked a library too much.
I suggest you try to modify the makefile like this now: (keep the 2 changes you made before)

- Put a "#" before CFLAGS
-...
Forum: Bioinformatics 08-03-2014, 06:06 AM
Replies: 34
Views: 14,590
Posted By Cytosine
From what I see in the error report you did not...

From what I see in the error report you did not make the proper adjustments in the Makefile.

Did you set -D_CURSES_LIB=1 to -D_CURSES_LIB=0 ?

and added the "#" in the following line?...
Forum: Bioinformatics 08-03-2014, 02:15 AM
Replies: 34
Views: 14,590
Posted By Cytosine
Seems you're still missing the ncurses library. ...

Seems you're still missing the ncurses library.

On ubuntu-based system you'd just do:
sudo apt-get install libncurses5-dev libncursesw5-dev

But Cygwin is a little different...

Googling it...
Forum: RNA Sequencing 08-02-2014, 12:43 AM
Replies: 3
Views: 2,575
Posted By Cytosine
Exception in thread "Thread-1"...

Exception in thread "Thread-1" java.lang.NullPointerException
at uk.ac.babraham.FastQC.Sequence.FastQFile.readNext(FastQFile.java:141)
at...
Forum: Bioinformatics 08-01-2014, 04:02 AM
Replies: 2
Views: 6,143
Posted By Cytosine
Samtools does have a really great, almost...

Samtools does have a really great, almost instant, access to any region of the .bam file because of it's .bai index file.

If you want to extract coverage at a specific point in your genome, then...
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