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-   -   Bfast query (http://seqanswers.com/forums/showthread.php?t=4194)

kakar_nipun 03-01-2010 10:33 AM

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

nilshomer 03-01-2010 11:09 AM

Quote:

Originally Posted by kakar_nipun (Post 14745)
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 (Post 14745)

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.


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