mapping the filtered reads (unmapped reeads) on the genome using bowtie2
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9.1 years ago
zizigolu ★ 4.3k

Hey there,

I have a sam file containing unmapped reads, which bowtie option doese map my reads on genome?

RNA-Seq • 2.5k views
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9.1 years ago
michael.ante ★ 3.8k

Hi Sarah,

Bowtie needs the reads in one of the following file formats (according to the manual):

FASTQ, QSEQ, or FASTA.

You need to convert the unmapped reads. Tophat has a tool called bam2fastx; the bedtools have bamToFastq; both can do the job. Afterwards, you can run bowtie with the fastq-file as input.

Cheers,
Michael

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Thank you very much

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Michael,

I am in Windows then I can't tophat and bedtools...:(

Do you know another way in Windows?

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In case you don't work on patients' data, you can do a lot using Galaxy.

It gives you a lot unix-based tools to work with and a good usability.

I think there are some tutorials out there which can help you analysing your data with Galaxy.

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Thank you

I went across to galaxy-picard-sam to fastq, but I don't know from from I can load my sam file into galaxy to be converted to fastq or fasta.

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Please read the docs and have a look here: http://https://wiki.galaxyproject.org/Learn

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:)

Thanks

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