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9.3 years ago
zizigolu
★
4.3k
Hey there,
I have a sam file containing unmapped reads, which bowtie option doese map my reads on genome?
Hey there,
I have a sam file containing unmapped reads, which bowtie option doese map my reads on genome?
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
Michael,
I am in Windows then I can't tophat and bedtools...:(
Do you know another way in Windows?
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.
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.
Please read the docs and have a look here: http://https://wiki.galaxyproject.org/Learn
:)
Thanks