Question: Comparing experimental reads to reference reads in csv
0
gravatar for heather.watkins
3 months ago by
heather.watkins0 wrote:

Hello,

I have a file with experimental reads I have cleaned (currently in fastqsanger format. I would like to match them to sequences I have stored in a csv file. I would also like to count the number of duplicates per matched sequence. Can you suggest a workflow to get this done?

Thank you. I am very new to this and all help is much appreciated!

Heather Watkins

fasta bam mark duplicates csv • 154 views
ADD COMMENTlink modified 12 weeks ago • written 3 months ago by heather.watkins0
0
gravatar for Jennifer Hillman Jackson
3 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Convert your reference sequences from cvs format to tabular format, then fasta format. It can then be used as a custom reference genome with tools, including mapping tools.

FAQ: https://galaxyproject.org/learn/custom-genomes/

Galaxy tutorials: https://galaxyproject.org/learn/

Thanks! Jen, Galaxy team

ADD COMMENTlink written 3 months ago by Jennifer Hillman Jackson25k

Thank you Jennifer. Your reply was very helpful ... so I'm back for more advice.

I was able to upload my reference genome in tabular format, convert to fasta, and then per the FAQ link you gave me, I used NGS Picard: Normalize fasta on it.

My reads , after using Trimmomatic on them, were in fastqsanger format. I mapped them to the custom genome using NGS Mapping: Map with BWA-MEM, successfully. However, when I try to use NGS Picard: Mark Duplicates, I get this fatal error:

Fatal error: Exit code 1 () Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/jobdir/019/250/19250644/_job_tmp -Xmx7g -Xms256m [Thu Apr 26 18:47:14 CDT 2018] picar

Do you have any idea why I am running into this error?

Thank you, Heather

ADD REPLYlink written 12 weeks ago by heather.watkins0

Hi - Could you please send in a bug report from the error dataset? This is how: https://galaxyproject.org/support/tool-error/ Thanks!

ADD REPLYlink written 12 weeks ago by Jennifer Hillman Jackson25k
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