ROI_Mapping: difference between Mapped ROI total and Mapped ROI total (bp)

NGSBabe · 02-03-2016, 10:25 PM

Hello,
I am new to PacBio and SMRT sequencing. Today I submit the job through SMRT portal: ROI_mapping and received the analysis back. However, on the job metrics, it showed Mapped ROI total = 53075 and Mapped ROI total (bp) = 127,933,383. What is different between these two terms? I am so confused.

Please help!

Thanks in advance.

rhall · 02-04-2016, 02:51 PM

The first is the number of reads, the second the number of base pairs mapped.

NGSBabe · 02-04-2016, 04:51 PM

Quote:

Originally Posted by rhall

The first is the number of reads, the second the number of base pairs mapped.

Thank you for your reply. But the number of reads meaning number of "base" read, is it correct?

The number of base pairs should be twice of the number of reads but in this case is not.

Can you clarify me on this?

Thank you very much.

rhall · 02-04-2016, 06:47 PM

A read is the fragment of DNA being sequenced, on pacbio this is not a fixed length, but is dependent on how the DNA was fragmented and if specific sizes of fragments are selected for. The number of mapped bases is the number of individual bases (ACGT) that map to the reference. Mapped bases / mapped reads = mean read length, in this case ~2,000 with is consistent with a short pacbio library.

NGSBabe · 02-06-2016, 09:05 PM

Quote:

Originally Posted by rhall

A read is the fragment of DNA being sequenced, on pacbio this is not a fixed length, but is dependent on how the DNA was fragmented and if specific sizes of fragments are selected for. The number of mapped bases is the number of individual bases (ACGT) that map to the reference. Mapped bases / mapped reads = mean read length, in this case ~2,000 with is consistent with a short pacbio library.

Thank you very much for your reply. Really appreciated!

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02-03-2016, 10:25 PM	#1
NGSBabe Junior Member Location: CA Join Date: Feb 2016 Posts: 3	ROI_Mapping: difference between Mapped ROI total and Mapped ROI total (bp) Hello, I am new to PacBio and SMRT sequencing. Today I submit the job through SMRT portal: ROI_mapping and received the analysis back. However, on the job metrics, it showed Mapped ROI total = 53075 and Mapped ROI total (bp) = 127,933,383. What is different between these two terms? I am so confused. Please help! Thanks in advance.

02-04-2016, 02:51 PM	#2
rhall Senior Member Location: San Francisco Join Date: Aug 2012 Posts: 322	The first is the number of reads, the second the number of base pairs mapped.

02-04-2016, 06:47 PM	#4
rhall Senior Member Location: San Francisco Join Date: Aug 2012 Posts: 322	A read is the fragment of DNA being sequenced, on pacbio this is not a fixed length, but is dependent on how the DNA was fragmented and if specific sizes of fragments are selected for. The number of mapped bases is the number of individual bases (ACGT) that map to the reference. Mapped bases / mapped reads = mean read length, in this case ~2,000 with is consistent with a short pacbio library.