Alignment and consensus from mapped reads (Ion PGM

Question: Alignment and consensus from mapped reads (Ion PGM - Ampliseq Custom Panel)

3.8 years ago by

United States

lkothera • 10 wrote:

I have an Ion Torrent Ampliseq Custom panel of 28 Culex genes that I have run on our Ion PGM. It's a small pilot project and I don't need to map against the whole genome (currently in the form of supercontigs), just my fasta file of 28 genes. I'd like to align the reads and get a consensus for each gene.

I have the PGM output as fastq files. Here's what I've done so far: used FastQ Groomer, Filtered those results on their quality scores, converted the FastQ results to FastA, and then mapped those reads using Lastz. I'm mapping the reads to my fasta file that has the sequences of the 28 genes in it.

That all seems to work. If you can see job #52 in my history, you can see the reads and that they are organized by gene (ex. CPIJ005953). I'm having trouble aligning the reads for each gene and then exporting a consensus. It's almost like my output is sort of a SAM file, but not enough of one to convert it to a BAM file. Can anyone advise? The data are for one individual, if that makes any difference.

Thanks,

Linda

consensus alignment • 1.8k views

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modified 3.8 years ago • written 3.8 years ago by lkothera • 10

3.8 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The complete set of wrapped assembly tools for Galaxy can be found in the tool shed under the category "Assembly". Please see:
http://usegalaxy.org/toolshed

If more adventurous, you can also review tool options in the Test tool shed here:
http://testtoolshed.g2.bx.psu.edu/

These tools are for use in a local or cloud Galaxy. Assembly tools are not supported on the public Main or Test Galaxy instances at this time.
http://wiki.galaxyproject.org/BigPicture/Choices

Best, Jen, Galaxy team

ADD COMMENT • link written 3.8 years ago by Jennifer Hillman Jackson ♦ 25k

3.8 years ago by

lkothera • 10

United States

lkothera • 10 wrote:

Thanks for your answer. Is there a particular tool that you think is worth trying? I looked over the list and nothing was obvious.

Linda

ADD COMMENT • link written 3.8 years ago by lkothera • 10

I've haven't performed an assembly on this data type myself, but have heard that MIRA is a good choice. This is in the tool shed.
https://toolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
http://sourceforge.net/projects/mira-assembler/ Documentation for 3rd party tool

Also, I think that TMAP is a better mapper choice for this sort of data. The tool is also in the tool shed.
https://toolshed.g2.bx.psu.edu/view/nilshomer/tmap_wrapper
https://github.com/iontorrent/TS/tree/master/Analysis/TMAP Documentation for 3rd party tool

But I wouldn't just start there. Better to review some recent publications and see what others are using for Methods. You might also ask on the Biostars forum (https://www.biostars.org) or even Seqanswers (http://seqanswers.com/) about which active researchers do the same general process are using, then compare answers with what is wrapped for Galaxy and decide now to proceed. (this forum focuses on Galaxy).

Best, Jen, Galaxy team

ADD REPLY • link written 3.8 years ago by Jennifer Hillman Jackson ♦ 25k

3.8 years ago by

lkothera • 10

United States

lkothera • 10 wrote:

Good ideas. Thanks for the feedback, Jen. It is appreciated.

Linda

ADD COMMENT • link written 3.8 years ago by lkothera • 10

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