goldrush for generating UMI consensus? about goldrush HOT 6 CLOSED

In which case you will have to change some GoldRush settings as it has not been tested on molecules that short before. Is the gene 600-700 bp long or the pacbio reads?

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In which case, I would recommend foregoing the goldrush pipeline and just running GoldPolish by selecting a high quality base read (i.e. golden path read) to polish.

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Thanks for your interest.

I want to clarify. The input reads would be all the sequences with the same UMI (derived from the same template molecule)? Assuming you can estimate the template molecule length, GoldRush could work for your purpose. How long are these molecules typically?

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Hello,

Thanks for the quick reply. Yes, all the reads are from the same template molecule bearing the same UMI sequence. This library is prepared from a single target gene. The reason why we decided to sequence using long reads is to capture SNPs that have been introduced. Even if we do not do a targeted sequencing we should be good. For this library, the sequence should be around 570-600 bp.

Thank you.

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The gene is around 525 nucl long with a 90 bp long barcode.

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This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your interest in GoldRush!

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