mapping the filtered reads (unmapped reeads) on the genome using bowtie2
1 answer
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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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.
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michael.ante
Please read the docs and have a look here: http://https://wiki.galaxyproject.org/Learn
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