mapping the filtered reads (unmapped reeads) on the genome using bowtie2

Question

[zizigolu]

Hey there,

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

Answer 1

[michael.ante]

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

[zizigolu]

Thank you very much

[zizigolu]

Michael,

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

Do you know another way in Windows?

[michael.ante]

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.

[zizigolu]

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.

[michael.ante]

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

[zizigolu]

:)

Thanks