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


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 • 298 views
ADD COMMENTlink modified 7 months ago • written 7 months ago by heather.watkins0
gravatar for Jennifer Hillman Jackson
7 months ago by
United States
Jennifer Hillman Jackson25k wrote:


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.


Galaxy tutorials:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 7 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: -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 7 months ago by heather.watkins0

Hi - Could you please send in a bug report from the error dataset? This is how: Thanks!

ADD REPLYlink written 7 months ago by Jennifer Hillman Jackson25k
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