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Mapping with Fasta vs fastq

Hey Everyone, I am trying to map small RNAs to a genome using Bowtie1. I initially did this with the following command and with a fastq file. But this time i want to use a fasta file and don't know if the command should change or remain the same. I tried and it didn't work though. The bowtie -h is not really clear to me. Thanks 

./bowtie /Users/bt1_Index   /Users/Whole.clipped.fastq --un un-mapped.fastq --al mapped.fastq -S Amphioxus.male.mapped.sam

NOte: this time i am using fasta instead of fastq

fasta fastq mapping bowtie1 command
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updated by GenoMax GenoMax • written by jaqx008 jaqx008

In case of fastq: bowtie [options]* <ebwt> {-1 <m1> -2 <m2> | --12 <r> | --interleaved <i> | <s>} [<hit>]
should not -1 -2 or --12 used before /Users/Whole.clipped.fastq

In case of fasta:

-f
The query input files (specified either as m1 and m2, or as s) are FASTA files (usually having extension .fa, .mfa, .fna or similar). All quality values are assumed to be 40 on the Phred quality scale.

If it did not work, what was the error?

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written by Medhat Medhat

Bellow is the command I just tried and it yielded a zero byte file.

bowtie .fasta --un Amph.unmapped.pi.fasta --al Amph.mapped.pi.fasta -S male.mappedfasta.sam
• 1 views • link
written by jaqx008 jaqx008

I just found out that I needed to specify -f so bowtie could recognize the fasta and that worked. Thanks for your contribution

• 1 views • link
written by jaqx008 jaqx008

Yes I told you that in the comment above :)

• 1 views • link
written by Medhat Medhat

Oh. My bad. I guess I just read the body of the message. Thanks again

• 1 views • link
written by jaqx008 jaqx008

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