hi all,
i am working on a project that i should find SNPs in the exome. so i installed Bowtie and i run it normaly with a set of reads. the result is in text format.
Now i want to work with Samtools to map this reads on the genome and to find SNPs. I took a look on samtools manual, but its so complicated and i dont know how do i start.
Its mentioned that samtools supports SAM/BAM format as input, but i think i didnt understand the right way to proceed with samtools, like : what format should i get after using Bowtie to be the samtools's input, and then what should i do with that input ....
so i will be very thankfull if someone could tell me those steps to do, cz seaching on the web its not always the best way.
thanks in advance
wassim
i am working on a project that i should find SNPs in the exome. so i installed Bowtie and i run it normaly with a set of reads. the result is in text format.
Now i want to work with Samtools to map this reads on the genome and to find SNPs. I took a look on samtools manual, but its so complicated and i dont know how do i start.
Its mentioned that samtools supports SAM/BAM format as input, but i think i didnt understand the right way to proceed with samtools, like : what format should i get after using Bowtie to be the samtools's input, and then what should i do with that input ....
so i will be very thankfull if someone could tell me those steps to do, cz seaching on the web its not always the best way.
thanks in advance
wassim
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