SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Novoalign query arkal General 2 10-03-2011 05:14 PM
cufflinks query seq_newbie Bioinformatics 0 07-15-2011 07:25 AM
BFAST bfast.submit.pl configuration epigen Bioinformatics 1 03-18-2011 06:51 AM
strand of query and mate valei Illumina/Solexa 1 09-27-2010 04:36 AM
BEDTools..coverageBed query Siva Bioinformatics 2 08-18-2010 11:10 AM

Reply
 
Thread Tools
Old 03-01-2010, 09:33 AM   #1
kakar_nipun
Junior Member
 
Location: texas,us

Join Date: Jul 2009
Posts: 3
Default Bfast query

Hi

I was trying to create indices for the reference genome using bfast 0.6.3.c and also trying to convert the reads.

Convert the reference:
bfast-0.6.3c/bfast/bfast fasta2brg -f microbial.fa

The above command airs out with an error and the error file has the following few last lines as output:
[----
[-----53
[-----540,-
[-----542,----2000000]
[-----545,----2000000]
[-----546,----------0]Base:[X]
************************************************************
In function "RGBinaryRead": Fatal Error[OutOfRange]. Variable/Value: original.
Message: Not a valid base pair.
***** Exiting due to errors *****
************************************************************

Can someone point out as to what might be the problem, i guess it is complaining about an invalid base, X in the sequence. How can i workaround this?

Convert the reads
perl /code/orange/BFAST/bfast-0.6.3c/scripts/ill2fastq.pl

what command line options should I choose to convert a file with the name rna_qseq.txt ?

Thanks,
Nipun
kakar_nipun is offline   Reply With Quote
Old 03-01-2010, 10:09 AM   #2
nilshomer
Nils Homer
 
nilshomer's Avatar
 
Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285
Default

Quote:
Originally Posted by kakar_nipun View Post
Hi

I was trying to create indices for the reference genome using bfast 0.6.3.c and also trying to convert the reads.

Convert the reference:
bfast-0.6.3c/bfast/bfast fasta2brg -f microbial.fa

The above command airs out with an error and the error file has the following few last lines as output:
[----
[-----53
[-----540,-
[-----542,----2000000]
[-----545,----2000000]
[-----546,----------0]Base:[X]
************************************************************
In function "RGBinaryRead": Fatal Error[OutOfRange]. Variable/Value: original.
Message: Not a valid base pair.
***** Exiting due to errors *****
************************************************************

Can someone point out as to what might be the problem, i guess it is complaining about an invalid base, X in the sequence. How can i workaround this?
Nipun
You can try the following to see if Xs are present.
Code:
grep "X" <ref.fa>
If so, you need to remove all Xs from your reference FASTA:
Code:
sed -i s_X_N_g <ref.fa>

Quote:
Originally Posted by kakar_nipun View Post

Convert the reads
perl /code/orange/BFAST/bfast-0.6.3c/scripts/ill2fastq.pl

what command line options should I choose to convert a file with the name rna_qseq.txt ?

Thanks,
Nipun
Can you try
Code:
perl ill2fastq.pl -q rna > out.fastq
This code is typically used on the original "qseq" files.
nilshomer is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 08:14 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO