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Forum: RNA Sequencing 04-23-2014, 12:43 AM
Replies: 0
Views: 1,134
Posted By sridhar28
Diff Genes from Cuffdiff output

Dear All,

i have Rna seq data drug treated in 4 diff time interval. my cuffdiff output gives more than 20000 significant genes. I used genes.gtf from ucsc as gtf input to cuffdiff.

how to get...
Forum: Bioinformatics 10-23-2013, 02:48 AM
Replies: 2
Views: 3,430
Posted By sridhar28
How to identify the Up and down Regulated genes from Cuff diff output

Dear All,

How to identify the Up and down regulated genes from the diff genes, I got diffgenes using Cummerbund codes.

In my diff_gene.txt file could see most of the log2fold change values are...
Forum: Bioinformatics 08-12-2013, 12:44 AM
Replies: 2
Views: 3,134
Posted By sridhar28
Dear Simon, I installed libcurl-devel and...

Dear Simon,

I installed libcurl-devel and now it works.. cummeRbund is installed now..
thank you for the suggestion..

Thanks
Sridhar
Forum: Bioinformatics 08-11-2013, 11:13 PM
Replies: 2
Views: 3,134
Posted By sridhar28
Warning messages in software during installing library package

Dear users,
I am trying to install cummeRbund library in my R latest version 3

i tried giving

source("http://bioconductor.org/biocLite.R")

biocLite("cummeRbund")

After installing...
Forum: Bioinformatics 07-28-2013, 08:24 PM
Replies: 1
Views: 5,059
Posted By sridhar28
R installation Problem

Dear Users,

I am trying to install R package(R-3.0.1) in my Linux Machine Redhat(6.0)
After unzip and giving command ./configure.. it run for sometime and finally i got

R is now configured...
Forum: Bioinformatics 07-28-2013, 08:07 PM
Replies: 3
Views: 1,709
Posted By sridhar28
hello Jackie, Thanks for the reply.. i could...

hello Jackie,
Thanks for the reply.. i could run GATK in commandline, i am getting results in commanline option but my task is to run it on galaxy.. so i am trying on it..

Could you please...
Forum: Bioinformatics 07-28-2013, 07:45 PM
Replies: 3
Views: 1,709
Posted By sridhar28
GATK in Galaxy

Dear Users,

I am running GATK (beta ) Unified Genotyper module in galaxy local interface to get the indels and SNP.

I placed the jar file in (/galaxy-dist/tool-data/shared/jars/gatk) and i...
Forum: Bioinformatics 06-17-2013, 12:53 AM
Replies: 6
Views: 2,819
Posted By sridhar28
Thanks for your suggestions. after...

Thanks for your suggestions. after AddorReplaceGroup from picard running GATK ..

the output is like

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT human
INFO ...
Forum: Bioinformatics 06-13-2013, 01:32 AM
Replies: 6
Views: 2,819
Posted By sridhar28
Hi newbie, thanks for you reply.. you...

Hi newbie,

thanks for you reply..

you mean instead of using the human genome fasta file i can use the .dict file while running the Unified Genotyper?
Also could you tell how to have "Read...
Forum: Bioinformatics 06-11-2013, 07:43 PM
Replies: 6
Views: 2,819
Posted By sridhar28
Hi, Actually i am running it in galaxy...

Hi,
Actually i am running it in galaxy interface. I am using Unified Genotyper module in GATK.
in backend i got the command.

python /illumina/data/galaxy/galaxy-dist/tools/gatk/gatk_wrapper.py ...
Forum: Bioinformatics 06-11-2013, 12:53 AM
Replies: 6
Views: 2,819
Posted By sridhar28
GATK error

Dear All,

I am using GATK for first time. i installed galaxy locally and running the softwares in it.
I am using Unified Genotyper module. my Gatk version is (GenomeAnalysisTK-2.5-2-gf57256b)...
Forum: RNA Sequencing 05-30-2013, 11:05 PM
Replies: 12
Views: 24,801
Posted By sridhar28
samtools installation : problem"gzopen64"

Hi,
I face the same problem even after reinstalling the zlib i am getting error as "undefined reference to `gzopen64' "

Thanks for any suggestions
Forum: Bioinformatics 05-30-2013, 09:18 PM
Replies: 7
Views: 4,046
Posted By sridhar28
Hi Geno, Thanks for the links.. i am...

Hi Geno,

Thanks for the links..

i am using redhat linux system..
after installing again i am facing same errors.. any thoughts??

samtools binary will be created only after installing the...
Forum: Bioinformatics 05-30-2013, 04:28 AM
Replies: 7
Views: 4,046
Posted By sridhar28
Hi geno, Thank you for the reply. I...

Hi geno,

Thank you for the reply.

I dint install those library.. could you please tell how to install it??

Thanks
Sridhar
Forum: Bioinformatics 05-30-2013, 03:48 AM
Replies: 7
Views: 4,046
Posted By sridhar28
Hi, I face same problem as mentioned. i am...

Hi,
I face same problem as mentioned. i am installing samtools version0.19 .
The Error i am getting is
warning: #warning "No curses library is available; tview with curses is disabled."
gcc -c...
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