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Question: mapping sanger sequencing files
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gravatar for yasharsad
2.7 years ago by
yasharsad • 0
yasharsad • 0 wrote:

I have over 600 ab1 files generated by sanger sequencing. they represent different splicing forms across herpes virus genome. what is the best way of mapping them on the genome and visualizing them?

The sequences need clipping too, as they all have bits from the vector sequenced with them.

I have tried usual tools available for sanger sequencing. but they are not able to map the files on the genome because of the splicing site in the middle of the genome.

Many thanks for your help and advise.
assembly rna-seq • 756 views
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modified 2.7 years ago • written 2.7 years ago by yasharsad • 0
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gravatar for Jennifer Hillman Jackson
2.7 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

For QA (trimming, adaptor, etc), see the tools in the group NGS: QC and manipulation at http://usegalaxy.org. Any of these can be added to a local or cloud Galaxy from the Tool Shed (as admin) if you happen to be working elsewhere.

For mapping, have you tried the mapping tools in the group NGS: RNA Analysis? HISAT2, Tophat

Thanks, Jen, Galaxy team
ADD COMMENT • link modified 2.7 years ago • written 2.7 years ago by Jennifer Hillman Jackson ♦ 25k
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gravatar for yasharsad
2.7 years ago by
yasharsad • 0
yasharsad • 0 wrote:

Hi Jen Many thanks for the guidence. I will try the tools that you have suggested. Yashar
ADD COMMENT • link written 2.7 years ago by yasharsad • 0
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