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Forum: Bioinformatics 03-15-2012, 12:39 PM
Replies: 1
Views: 1,639
Posted By CS Student
I was able to solve this issue using the...

I was able to solve this issue using the following two options:

1. --qv-offset 64: Interpret qvs in fastq input as PHRED+<value>. The default is 33 for colour space and 64 for letter space.
...
Forum: General 03-15-2012, 11:39 AM
Replies: 2
Views: 1,548
Posted By CS Student
Thanks a lot for your help. I found some tools to...

Thanks a lot for your help. I found some tools to convert from FASTAQ to FASTA.
Forum: Bioinformatics 03-15-2012, 11:37 AM
Replies: 1
Views: 1,639
Posted By CS Student
SHRiMP with FASTAQ input

Dear all,

I am trying to run SHRiMP with FASTAQ input files using the -Q option.

Here is the command I am using:

/home/user/SHRiMP_2_2_2/bin/gmapper-ls ...
Forum: General 03-13-2012, 10:42 AM
Replies: 2
Views: 1,548
Posted By CS Student
Short-reads in FASTA format

Hi,

I need to run some experiments on short-reads in fasta format. However, all the sources I found is using FASTAQ format for short-reads. I tried some tools for converting FASTAQ to FASTA, but...
Forum: General 01-21-2012, 04:10 AM
Replies: 5
Views: 2,064
Posted By CS Student
Thank you very much for your explainations. This...

Thank you very much for your explainations. This is all what I wanted to know about # reads and #bases.
Forum: General 01-20-2012, 07:54 AM
Replies: 5
Views: 2,064
Posted By CS Student
#bases & # reads

Hi,

I am new to bioinformatics and appreciate your help answering this question.

I have a reads file [a sample is attached] and want to count the number of #bases and number of reads in this...
Forum: General 01-11-2012, 12:12 PM
Replies: 1
Views: 1,452
Posted By CS Student
BFAST malloc error

Hi,

I am getting the below memory corruption error when trying to run BFAST on a 4GB RAM machine.

Could you please advise?

Thanks.
=========================================

*** glibc...
Forum: General 11-28-2011, 10:27 PM
Replies: 1
Views: 1,525
Posted By CS Student
BFAST- Error in RGMatch.c

Dear all,

I am trying to use BFAST.

Could you please advise on what could be the reason for getting the below error?

bfast: ../bfast/RGMatch.c:155: RGMatchPrint: Assertion `m->readLength >...
Forum: General 11-27-2011, 11:22 PM
Replies: 3
Views: 1,491
Posted By CS Student
It works fine now using "make clean" before...

It works fine now using "make clean" before "make".

Thanks a lot Nils!
Forum: General 11-27-2011, 09:26 AM
Replies: 3
Views: 1,491
Posted By CS Student
Error in Compiling BFAST

Hi,

I am trying to compile the source code of BFAST and I am getting the below error message when trying to "make". Appreciate any advice on the error message.

* I use "./configure" before...
Forum: General 10-08-2011, 11:06 AM
Replies: 6
Views: 2,252
Posted By CS Student
Thanks Michael. I tried with double...

Thanks Michael.

I tried with double quotations as you did and added the "/" character at the end of my path and it worked.

I have another problem now. I get the following error [at the end of...
Forum: General 10-08-2011, 12:28 AM
Replies: 6
Views: 2,252
Posted By CS Student
I tried removing the apostrophes, but still...

I tried removing the apostrophes, but still getting the same error!

Could you please advise on another solution?

Thanks.
Forum: General 10-07-2011, 06:15 AM
Replies: 6
Views: 2,252
Posted By CS Student
BFAST- specifying tmpDir parameters

Hi,

I am trying to use the (-T) option in the bfast "match" command to specify the directory to which temporary files will be written instead of the default directory (current directory), but not...
Forum: General 05-26-2011, 11:56 AM
Replies: 2
Views: 1,596
Posted By CS Student
Thanks for your reply.

Thanks for your reply.
Forum: General 05-21-2011, 12:40 PM
Replies: 2
Views: 1,596
Posted By CS Student
Warning message- BFAST

Dear all,

I am getting the below warning message when trying to run the BFAST program. I would appreciate any help explaining for me the reason for getting this message?

Thanks....
Forum: Bioinformatics 04-03-2011, 01:36 PM
Replies: 10
Views: 5,763
Posted By CS Student
Many thanks for your replies Nils, appreciated. ...

Many thanks for your replies Nils, appreciated.

As far as I understood from the example explanation, I need a reference genome in FASTA format data in addition to the short read files.

I am...
Forum: Bioinformatics 04-03-2011, 03:32 AM
Replies: 10
Views: 5,763
Posted By CS Student
Thanks Nils for your reply. So, if I want to...

Thanks Nils for your reply.

So, if I want to run an example to try the BFAST code, from where I can get a similar data set sample??

Thanks..
Forum: Bioinformatics 04-02-2011, 11:47 PM
Replies: 10
Views: 5,763
Posted By CS Student
Nils and I meant the files which have been taken...

Nils and I meant the files which have been taken down, not the post.

Thanks..
Forum: Bioinformatics 04-02-2011, 09:57 PM
Replies: 10
Views: 5,763
Posted By CS Student
Thanks Nils for your reply. Why it has been...

Thanks Nils for your reply.
Why it has been taken down?

If it is not possible to get it, could you please point me to another similar data set which I can use to run the same example in the...
Forum: Bioinformatics 04-02-2011, 01:55 PM
Replies: 10
Views: 5,763
Posted By CS Student
BFAST: Need "Phi X 174" file example dataset

Hi all,

I am trying to download an example data set for BFAST, which is Phi X 174 from the BFAST main page but the link is broken....
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