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Forum: RNA Sequencing 08-17-2015, 08:57 AM
Replies: 1
Views: 2,584
Posted By csmatyi
Hello everybody, I have a line from...

Hello everybody,

I have a line from genes.fpkm_tracking from cuffdiff output:

XLOC_000001 - - XLOC_000001 NM_008866 TSS1 chr1:4807892-4846735 - - ...
Forum: Bioinformatics 07-17-2014, 08:36 AM
Replies: 2
Views: 886
Posted By csmatyi
Hello everyone, I have a statistics question: ...

Hello everyone, I have a statistics question:

I have a data set:

1
1
1
0
1
1
Forum: Bioinformatics 07-02-2014, 01:18 PM
Replies: 3
Views: 1,062
Posted By csmatyi
can cuffdiff be run to examine individual transcript results?

Hello everybody,

Can cuffdiff be run so as to do differential gene expression not on a gene by gene basis, as it does normally, but on a transcript basis?

In other words, cufflinks produces...
Forum: Literature Watch 06-10-2014, 04:47 PM
Replies: 2
Views: 13,092
Posted By csmatyi
where can I download a whole Neanderthal genome from?

where can I download a whole Neanderthal genome from?

That is, I'd preferably like a fasta file, not fastq or millions of reads.

By the way, this Altai Neanderthal woman whole genome, it only...
Forum: Bioinformatics 05-16-2014, 11:27 AM
Replies: 8
Views: 6,187
Posted By csmatyi
Hi crazyhottommy, I have no sudo privilege...

Hi crazyhottommy,

I have no sudo privilege on the server I'm on.
Basically, how do I install it in a simple way without any special necessary privileges needed?
Forum: Bioinformatics 05-15-2014, 07:13 AM
Replies: 8
Views: 6,187
Posted By csmatyi
Hi, maybe you can help me with an installation...

Hi, maybe you can help me with an installation problem I have with bcbio-nextgen. I want to install it on linux, but I get this error:

-----

Error: Cannot install tabix because conflicting...
Forum: Bioinformatics 04-17-2014, 12:43 PM
Replies: 10
Views: 3,730
Posted By csmatyi
The ones marked with j in the 3rd column are new...

The ones marked with j in the 3rd column are new transcripts, according to the cuffcompare manual.
Forum: Bioinformatics 04-12-2014, 12:05 PM
Replies: 10
Views: 3,730
Posted By csmatyi
novel INDELs, splice variants, transcripts

Dear everybody,

I have been running the tophat->cufflinks->cuffcompare software in order to find new INDELs, splice variants, and transcripts. This is a screenshot of my cuffcompare results:
...
Forum: Bioinformatics 02-07-2014, 08:58 AM
Replies: 23
Views: 58,947
Posted By csmatyi
oh it's so appropriate

oh it's so appropriate
Forum: Clinical Sequencing 12-05-2013, 07:20 AM
Replies: 0
Views: 8,419
Posted By csmatyi
ISAcreatorConfigurator

Hello everybody,

I have a big problem:

I have the Bioinvindex web app running. I also made same isatab files and uploaded them to my website. Also a test file, BII-S-3 from the isatools website...
Forum: Bioinformatics 11-15-2013, 08:43 AM
Replies: 0
Views: 1,036
Posted By csmatyi
SOAP pipeline

Hello everybody,

I would like to know if there is a description of a SOAP pipeline out there anywhere.

I have 2 paired end fastq files. I want to align these to the hg19 genome, and find SNPs....
Forum: Bioinformatics 11-14-2013, 12:22 PM
Replies: 11
Views: 7,250
Posted By csmatyi
You are a genius! :D

You are a genius! :D
Forum: Bioinformatics 11-14-2013, 12:21 PM
Replies: 11
Views: 7,250
Posted By csmatyi
Hello Tomas, I can't beleive it. I tried what you...

Hello Tomas, I can't beleive it. I tried what you said and it didn't work for me. I even copied out the dash from in front of the a parameter, and it is a single dash, not a double one. Where did you...
Forum: General 08-16-2013, 08:10 AM
Replies: 2
Views: 6,058
Posted By csmatyi
human gene nomenclature

Dear everybody,

Can anyone suggest good online databases which house information on gene nomenclature in human? Synonyms databases?

Thanks, csmatyi
Forum: RNA Sequencing 08-05-2013, 07:14 AM
Replies: 5
Views: 3,842
Posted By csmatyi
tophat 2.0.9.

Dear all,

I keep getting the following error message when using tophat:

Error running 'long_spanning_reads':/util/opt/tophat/2.0.9/gcc/4.4.7/bin/long_spanning_reads: error while loading shared...
Forum: Bioinformatics 03-07-2013, 06:19 AM
Replies: 3
Views: 2,513
Posted By csmatyi
we got it to run

We got the whole pipeline to run. Did you use an appropriate gff file and genome sequence file? What species are you studying? Maybe they have an appropriate species gff file for you on the mirdeep...
Forum: Bioinformatics 02-01-2013, 06:42 AM
Replies: 16
Views: 6,694
Posted By csmatyi
How do you run RNAfold with a multifasta file...

How do you run RNAfold with a multifasta file producing multiple ps files, each with a sec structure file for each individual sequence? Plus, how do you print the energy values in the pdf?
Forum: Bioinformatics 01-17-2013, 01:02 PM
Replies: 4
Views: 1,243
Posted By csmatyi
Hello, <REF>/<DATA>/frag_reads_orig.fastb ...

Hello,

<REF>/<DATA>/frag_reads_orig.fastb
<REF>/<DATA>/frag_reads_orig.qualb
<REF>/<DATA>/frag_reads_orig.pairs
<REF>/<DATA>/jump_reads_orig.fastb
<REF>/<DATA>/jump_reads_orig.qualb...
Forum: Bioinformatics 01-16-2013, 02:07 PM
Replies: 1
Views: 1,392
Posted By csmatyi
you're not alone

you're not alone
Forum: Bioinformatics 10-05-2012, 09:46 AM
Replies: 16
Views: 8,320
Posted By csmatyi
Linux based at least level 2 RAID server, >5 Tb

Hello everyone,

We're looking to purchase a memory disk.
This disk must fulfill the following requirements:

- >= 5Tb memory
-min. RAID2, 3-4-5 would be better


To be used for backups,...
Forum: Bioinformatics 08-30-2012, 12:47 PM
Replies: 15
Views: 16,617
Posted By csmatyi
Hello, check the appropriate sra file at ncbi,...

Hello, check the appropriate sra file at ncbi, they will give you the length of the left and right reads and the insert mean and std!
Forum: Bioinformatics 08-30-2012, 11:58 AM
Replies: 5
Views: 5,424
Posted By csmatyi
I installed the binary version of tophat-2.0.4...

I installed the binary version of tophat-2.0.4 because the manual install failed because I wasn't able to install boost properly (for me this is a separate issue).

This is what I get after trying...
Forum: Bioinformatics 08-30-2012, 11:24 AM
Replies: 5
Views: 5,424
Posted By csmatyi
Hi, the same thing happens with me. I also tried...

Hi, the same thing happens with me. I also tried installing boost, but it doesn't make. I also tried running the binaries but I get the same error message.
Forum: Bioinformatics 08-27-2012, 08:57 AM
Replies: 13
Views: 8,874
Posted By csmatyi
I don't think that's a problem if the fastq file...

I don't think that's a problem if the fastq file gets bigger because the sra file is in binary anyway, which is more compact.
Forum: RNA Sequencing 10-20-2011, 10:39 AM
Replies: 4
Views: 3,144
Posted By csmatyi
Same problem for us over here! All of our...

Same problem for us over here! All of our p-values come out as 1.
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