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Question: Gain Sequences After Mapping Reads To A Reference Genome
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gravatar for zwp112358
5.6 years ago by
zwp112358 • 10
zwp112358 • 10 wrote:
Hi all, I would like to know if mapping reads to a reference genome, through galaxy, can generate the query genome sequence? I had mapped my reads from Illumina sequencer to a reference genome through both BWA and Bowtie on Galaxy public server platform(https://main.g2.bx.psu.edu/root ). As a result, i gained the SAM files. But, i can't find how to generate the resulted assemblied genome sequence. Is there anyone know this? Any reply will be very appreciated. Best regards. Weiping Weiping Zhang, Doctor candidate; School of bioengineering, Jiangnan University; Lihu Roads 1800#, WUXI, Jiangsu; Zip Code: 214122
bwa alignment bowtie • 1.6k views
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modified 5.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 5.6 years ago by zwp112358 • 10
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gravatar for Jennifer Hillman Jackson
5.6 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hello Weiping, The resulting SAM hits can be converted to intervals, and the intervals merged, and those regions extracted from the reference genome you mapped to. The tools to use would be: * NGS: SAM Tools -> Convert SAM to interval * Operate on Genomic Intervals -> Merge (although you can explore other tools in this group) * Fetch Sequences -> Extract Genomic DNA Note that this would not include any variation included in the original mapped fastq data itself. If you are interested variation (SNPs or Indels or both) in your data, then you want to use a mapping tool like BWA (or Bowtie2 in a local or cloud Galaxy), followed by a variant analysis tools. Several tool groups in the "NGS:*" section are for this purpose, such as those in the group " NGS: SAM Tools" (Mpileup, etc.). Hopefully this helps, Jen Galaxy team -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org
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