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Old 02-28-2012, 07:12 AM   #1
fc35802
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Question Doubt about .abi files and .fasta files

Hi,

I have Sanger reads on .abi format and NGS reads in .fastq format. They are both from the same bacteria.
I was thinking if I could convert .abi to fasta (I know how to do that) and convert my NGS reads to .fasta (I also know how to do that) and use both to do an alignment using bowTie (this programs can use a .fasta input, rigth? Unlike bwa)

Any thought about this?

Thanks in advance
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Old 02-28-2012, 08:29 AM   #2
maubp
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Why not use FASTQ rather than FASTA, that way you can keep the quality scores?

Both EMBOSS (see the seqret tool) and Biopython (Version 1.58 onwards, use Bio.SeqIO.convert) can convert from ABI to FASTQ.
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Old 02-28-2012, 10:05 AM   #3
kmcarr
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Quote:
Originally Posted by fc35802 View Post
Hi,

I have Sanger reads on .abi format and NGS reads in .fastq format. They are both from the same bacteria.
I was thinking if I could convert .abi to fasta (I know how to do that) and convert my NGS reads to .fasta (I also know how to do that) and use both to do an alignment using bowTie (this programs can use a .fasta input, rigth? Unlike bwa)

Any thought about this?

Thanks in advance
Why insist on using the same aligner? Bowtie & BWA are designed to align (relatively) short, NGS reads. They would not be my first choice for aligning Sanger reads. Use an appropriate alignment tool for each type of read then combine the results of those alignments.
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