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Question: Alignment Question
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gravatar for Michaela Lee
8.9 years ago by
Michaela Lee • 30
Michaela Lee • 30 wrote:
Hello, I was wondering if Galaxy can align Solexa reads to a reference sequence. If not, can I upload my alignment data from Maq onto Galaxy and somehow work with that data online? Also, can Galaxy tell me which parts of the reference sequence have no reads aligned to them? I am basically trying to figure out which parts were not sequenced and compare those sequences between different subjects. Thanks for your help. M
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modified 8.9 years ago by Anton Nekrutenko ♦ 1.7k • written 8.9 years ago by Michaela Lee • 30
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gravatar for Anton Nekrutenko
8.9 years ago by
Anton Nekrutenko ♦ 1.7k
Penn State
Anton Nekrutenko ♦ 1.7k wrote:
Michaela: Yes. Bowtie and BWA mappers will align illumina reads against a reference genome. Take a look at our quickie #7 at http://usegalaxy.org Thanks, anton galaxy team Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org
ADD COMMENT • link written 8.9 years ago by Anton Nekrutenko ♦ 1.7k
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gravatar for Anton Nekrutenko
8.9 years ago by
Anton Nekrutenko ♦ 1.7k
Penn State
Anton Nekrutenko ♦ 1.7k wrote:
Michaela: Sorry for delay in replying. Looks like you need to do this: 1. Map reads with bowtie using "try hard" option. 2. Leave -m option at -1 3. Set -k ridiculously high (e.g., 1000) 4. Once mapped filter SAM with "SAM Tools->Filter SAM on bitwise flag" filter tool using option as in the attached image
ADD COMMENT • link written 8.9 years ago by Anton Nekrutenko ♦ 1.7k
Thanks Anton! Everything works fine except the last step. The mapped regions could not be subtracted from the reference sequence file because that file is not in the same interval format. I tried to change the fasta file to an interval file using "edit attributes" but it didn't work. In fact, when I try to specify which column is the sequence and which is the identifier/name, it shows me that I only have 1 column to work with. I tried to change the fasta file to a tab file and then to an interval file but that didn't really work either. Any suggestions? Michaela
ADD REPLY • link written 8.9 years ago by Michaela Lee • 30
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