Question: mapping the filtered reads (unmapped reeads) on the genome using bowtie2
0
gravatar for A
4.5 years ago by
A3.6k
A3.6k wrote:

hey there,

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

 

rna-seq • 1.5k views
ADD COMMENTlink modified 4.5 years ago by michael.ante3.5k • written 4.5 years ago by A3.6k
1
gravatar for michael.ante
4.5 years ago by
michael.ante3.5k
Austria/Vienna
michael.ante3.5k wrote:

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

ADD COMMENTlink written 4.5 years ago by michael.ante3.5k

thank u very much

ADD REPLYlink written 4.5 years ago by A3.6k

Michael,

i am in wondows then i cant tophat and bedtools...:(

do u know another way in windows?

ADD REPLYlink written 4.5 years ago by A3.6k
1

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.

ADD REPLYlink written 4.5 years ago by michael.ante3.5k

thank you

i went across to galaxy-picard-sam to fastq, but i don konw from from i can load my sam file into galaxy to be converted to fastq or fasta...

ADD REPLYlink written 4.5 years ago by A3.6k
1

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

ADD REPLYlink written 4.5 years ago by michael.ante3.5k

:)

thanks

ADD REPLYlink written 4.5 years ago by A3.6k
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