Question: Converting pair-end dataset to fastq
0
gravatar for stephen.pak
3.4 years ago by
United States
stephen.pak0 wrote:

I'm new to galaxy and am trying to use the cloudmap workflow to conduct "Hawaiian variant mapping with WGS data". The WGS data was initially provided as pair-end data in two files. I converted the files to fastq.sanger using the "groomer" tool then joined the two files together using the "joiner" tool. When I perform the Hawaiian variant mapping workflow. Everything seems to work fine but the "scatter plots" of the SNP ratios always fail.  Any idea why this is happening? Is the WGS data in the correct format?

My "joined" pair-end reads look like this:

@NRCHBS-WDL30774:60:C3YYDANXX:8:1101:1447:1915 1:N:0:AAGACG

NGAAATCCTGGAGGGCCTGAATTTCAACCTCACGGAGATTCCGGAGGCTCAGATCCATGAAGGCTTCCAGGAACTCTTCTGAGTGGTACAACTTTTTAACATCCTCCAAAAACTTATCCACTAGCTTCAGGCCCTCGCTGAGGANNNNNNNN

+

#<<ABGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCCCBGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGG########

galaxy cloudmap • 938 views
ADD COMMENTlink modified 3.4 years ago by Jennifer Hillman Jackson24k • written 3.4 years ago by stephen.pak0
0
gravatar for Jennifer Hillman Jackson
3.4 years ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

As far as I know, you wouldn't ever want to map with the two ends of a paired set joined together. Instead, map them as as a paired dataset, inputing each of the two fastq files separately, but in the same run. Choose paired on the mapper tool form and you will see the options to add both in.

If you need more details with this particular pipeline, I can let you know that the authors offer group and direct support plus an FAQ. See the Cloudmap Page for contact details.
http://usegalaxy.org/u/gm2123/p/cloudmap

Hope this helps! Jen, Galaxy team

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by Jennifer Hillman Jackson24k

Thanks for your answer. I will try that now. Cheers, Stephen

On 10/16/14 12:23 PM, "Jennifer Hillman Jackson on Galaxy Biostar" <notifications@biostars.org> wrote:

Activity on a post you are following on Galaxy Biostar <http: biostar.usegalaxy.org="">

User Jennifer Hillman Jackson <http: biostar.usegalaxy.org="" u="" 254=""/> wrote Answer: Converting pair-end dataset to fastq <http: biostar.usegalaxy.org="" p="" 9313="" #9315=""> :

Hello,

As far as I know, you wouldn't ever want to map with the two ends of a paired set joined together. Instead, map them as as a paired dataset, inputing each of the two fastq files separately, but in the same run. Choose paired on the mapper tool form and you will see the options to add both in.

If you need more details with this particular pipeline, I can let you know that the authors offers group and direct support plus an FAQ. See the Cloudmap Page for contact details. http://usegalaxy.org/u/gm2123/p/cloudmap

Hope this helps! Jen, Galaxy team


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ADD REPLYlink written 3.4 years ago by stephen.pak0
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