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Forum: Bioinformatics 06-05-2014, 12:17 AM
Replies: 9
Views: 8,648
Posted By archi
Hi all, I'm also doing analysis of some nextgen...

Hi all, I'm also doing analysis of some nextgen data. right now,I'm handling fastq files of three experimental replicates and want to calculate their correlation(i.i correlation of the three...
Forum: Bioinformatics 06-02-2014, 01:06 AM
Replies: 10
Views: 10,152
Posted By archi
Hi all,I'm using SRA TOOLKIT VERSION 2.3.4 for a...

Hi all,I'm using SRA TOOLKIT VERSION 2.3.4 for a 64bit linux system, initially I was able to successfully convert sra to fastq but now I'm getting the following error message:

2014-06-02T08:58:01...
Forum: Bioinformatics 06-01-2014, 09:25 AM
Replies: 9
Views: 8,624
Posted By archi
I have around 4 Lac lines in my fastq file.So...

I have around 4 Lac lines in my fastq file.So while using readFastq I'm constantly getting an error message of unexpected number of lines.
Can someone please suggest how do I manipulate my reads...
Forum: Bioinformatics 05-24-2014, 01:49 AM
Replies: 9
Views: 8,624
Posted By archi
While using ShortRead package to read a fastq...

While using ShortRead package to read a fastq file what are the exact arguments to be put in the readFastq function?
and how do we segregate from so many reads only those which have a particular...
Forum: Bioinformatics 05-24-2014, 01:46 AM
Replies: 9
Views: 8,624
Posted By archi
okay,got it. thanks

okay,got it.
thanks
Forum: Bioinformatics 05-23-2014, 01:36 AM
Replies: 9
Views: 8,624
Posted By archi
I'm able to generate the fastq version of the sra...

I'm able to generate the fastq version of the sra file in the terminal.But how do I save its copy in my computer??

please reply asap
Forum: Bioinformatics 04-29-2014, 11:37 PM
Replies: 9
Views: 8,624
Posted By archi
I'm getting the following errors in using the...

I'm getting the following errors in using the readFastq function
readFastq("home/linux/sratoolkit.2.34-2-centos_linux64/bin",pattern="SRR039194_1.fastq")
Error: Input/Output
no input files found...
Forum: Bioinformatics 04-29-2014, 11:33 PM
Replies: 21
Views: 8,979
Posted By archi
now I'm getting the following errors in using the...

now I'm getting the following errors in using the readFastq function
readFastq("home/linux/sratoolkit.2.34-2-centos_linux64/bin",pattern="SRR039194_1.fastq")
Error: Input/Output
no input files...
Forum: Bioinformatics 04-29-2014, 11:30 PM
Replies: 21
Views: 8,979
Posted By archi
Now I'm getting following error in using...

Now I'm getting following error in using readFastq function:

readFastq("home/linux/sratoolkit.2.34-2-centos_linux64/bin",pattern="SRR039194_1.fastq")
Error: Input/Output
no input files found
...
Forum: Bioinformatics 04-29-2014, 09:57 PM
Replies: 21
Views: 8,979
Posted By archi
Yes,sure. after installing libxml,the main...

Yes,sure.
after installing libxml,the main problem was having libcurl on my system.As I'm working on linux,libcurl has to be explicitly installed and I did that using Ubuntu software center.After...
Forum: Bioinformatics 04-29-2014, 07:00 AM
Replies: 21
Views: 8,979
Posted By archi
Thanks a lot everyone. I have successfully...

Thanks a lot everyone. I have successfully installed ShortRead package on my system.
Forum: Bioinformatics 04-29-2014, 06:55 AM
Replies: 21
Views: 8,979
Posted By archi
I think I need libcurl (version 7.14.0 or higher)...

I think I need libcurl (version 7.14.0 or higher) as I'm working on linux but can't figure out how to do that. Can someone please suggest something asap.
thanks in advance
Forum: Bioinformatics 04-29-2014, 06:47 AM
Replies: 21
Views: 8,979
Posted By archi
I have installed libxml2-dev but now I'm getting...

I have installed libxml2-dev but now I'm getting these error.
Sorry for asking such basic doubts but please do help
Thanks a lot.

installing to...
Forum: Bioinformatics 04-29-2014, 06:30 AM
Replies: 21
Views: 8,979
Posted By archi
Also, can u please tell me how to install libcurl...

Also, can u please tell me how to install libcurl on ubuntu for R 3.0.2
Forum: Bioinformatics 04-29-2014, 06:26 AM
Replies: 21
Views: 8,979
Posted By archi
can u please elaborate??

can u please elaborate??
Forum: Bioinformatics 04-29-2014, 05:18 AM
Replies: 21
Views: 8,979
Posted By archi
Hi All, I have tried installing the ShortRead...

Hi All,
I have tried installing the ShortRead package many times now using
source("http://bioconductor.org/biocLite.R")
biocLite("ShortRead")
but everytime I get an error message when I use...
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