Bfast query

[kakar_nipun]

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]

Originally Posted by kakar_nipun

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.

grep "X" <ref.fa>

If so, you need to remove all Xs from your reference FASTA:

sed -i s_X_N_g <ref.fa>

Originally Posted by kakar_nipun

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

perl ill2fastq.pl -q rna > out.fastq

This code is typically used on the original "qseq" files.