Hello All,
First of all I am very new at this NGS sequence analysis.
I have a sff file generated by the 454 machine.
In it I have 500000 reads
200000 of them are <200bp
300000 of them are >200bp (but less than 600bp)
I want to use bwt to align the reads to a reference:
1) Do I have to separate the short reads from the longer ones? if yes what is the fastest way to do so?
2) What input files can I use with bwt. fasta? fastq?
The 454 machine did not give any fastq files. I made one using the perl script that came with bwt. (how reliable is that perlscript)?
at the moment I am issuing the following command:
a) index the reference first
bwa index -p ref_index -a is my_ref.fa (note: my reference is 1.5MB that is why I am using '-a is')
b) align the reads to reference
bwa aln -t 4 ref_index my_reads.fasta > my_reads.bwa
c) convert to SAM
bwa samse ref_index my_reads.bwa my_reads.fasta > my_reads.sam
Are steps a to c right?
I read that I should use 'bwa bwasw' to align long reads.
Any guidance you are able to provide is greatly appreciated!!!1
Thanks
Noah
First of all I am very new at this NGS sequence analysis.
I have a sff file generated by the 454 machine.
In it I have 500000 reads
200000 of them are <200bp
300000 of them are >200bp (but less than 600bp)
I want to use bwt to align the reads to a reference:
1) Do I have to separate the short reads from the longer ones? if yes what is the fastest way to do so?
2) What input files can I use with bwt. fasta? fastq?
The 454 machine did not give any fastq files. I made one using the perl script that came with bwt. (how reliable is that perlscript)?
at the moment I am issuing the following command:
a) index the reference first
bwa index -p ref_index -a is my_ref.fa (note: my reference is 1.5MB that is why I am using '-a is')
b) align the reads to reference
bwa aln -t 4 ref_index my_reads.fasta > my_reads.bwa
c) convert to SAM
bwa samse ref_index my_reads.bwa my_reads.fasta > my_reads.sam
Are steps a to c right?
I read that I should use 'bwa bwasw' to align long reads.
Any guidance you are able to provide is greatly appreciated!!!1
Thanks
Noah
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