Question: How to remove duplicate sequence
gravatar for pattythepsuwan
16 months ago by
pattythepsuwan0 wrote:

Our Ribo-seq libraries involved a PCR step (9 cycles of amplification) in order to get enough material to put on the sequencer. Because of this, we expect that many of the reads are actually exact duplicates of clones which are not real duplicates but arise as an artifact of PCR. Is there any option on Galaxy that I can use to remove the duplicate?

Sincerely, Patty Thepsuwan

rna-seq reads duplicate • 954 views
ADD COMMENTlink modified 16 months ago by Jennifer Hillman Jackson25k • written 16 months ago by pattythepsuwan0
gravatar for Jennifer Hillman Jackson
16 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello Patty,

Map the data, sort the BAM result, then run the tool NGS: SAMtools > RmDup. The tool group SAMtools also has tool options to mark and/or remove duplicates. To find all quickly, use the term "duplicates" in the tool panel search.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 16 months ago by Jennifer Hillman Jackson25k
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