SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Pacific Biosciences



Similar Threads
Thread Thread Starter Forum Replies Last Post
Coverage of ROI on TruSight ramujana Illumina/Solexa 1 04-11-2014 04:30 AM
Discrepancy between HTSeq-count counts and total mapped reads M_staats Bioinformatics 1 03-21-2013 06:16 AM
Extract mean mapped base phred quality by mapped location from BAM file ugm6hr Bioinformatics 2 10-05-2012 03:52 AM
BIG difference in number of genes mapped with tophat vs. casava 1.8.2 hmortens Bioinformatics 0 07-30-2012 07:24 AM
Paired-end reads mapped 50% while each pair reads mapped 80% zack80.liu Bioinformatics 3 03-03-2011 01:06 AM

Reply
 
Thread Tools
Old 02-03-2016, 09:25 PM   #1
NGSBabe
Junior Member
 
Location: CA

Join Date: Feb 2016
Posts: 3
Default 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.
NGSBabe is offline   Reply With Quote
Old 02-04-2016, 01:51 PM   #2
rhall
Senior Member
 
Location: San Francisco

Join Date: Aug 2012
Posts: 322
Default

The first is the number of reads, the second the number of base pairs mapped.
rhall is offline   Reply With Quote
Old 02-04-2016, 03:51 PM   #3
NGSBabe
Junior Member
 
Location: CA

Join Date: Feb 2016
Posts: 3
Default

Quote:
Originally Posted by rhall View Post
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.
NGSBabe is offline   Reply With Quote
Old 02-04-2016, 05:47 PM   #4
rhall
Senior Member
 
Location: San Francisco

Join Date: Aug 2012
Posts: 322
Default

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.
rhall is offline   Reply With Quote
Old 02-06-2016, 08:05 PM   #5
NGSBabe
Junior Member
 
Location: CA

Join Date: Feb 2016
Posts: 3
Default

Quote:
Originally Posted by rhall View Post
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!
NGSBabe is offline   Reply With Quote
Reply

Tags
pacbio, read of insert, rs ii, smrt sequencing

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 03:20 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO