Daniel:Notebook/ComboLock/2016-11-21: Difference between revisions
>Djacobse (Created page with "=Sequencing Results-Miseq 2016-11-17= Back to Calendar ==Circularization Optimization Testing (Started [[Daniel:Notebook/ComboLock/2016-10-31|O...") |
>Djacobse |
||
Line 18: | Line 18: | ||
==Cell Test with RCA (Started [[Daniel:Notebook/ComboLock/2016-11-7|Nov 7]])== | ==Cell Test with RCA (Started [[Daniel:Notebook/ComboLock/2016-11-7|Nov 7]])== | ||
Unfortunately, this winds up to the same problems as above. See the gallery below. | |||
<gallery perrow=2 heights=400px widths=400px> | |||
File:Miseq20161117-BaseQual-Ind25.png|Base qualities | |||
File:Miseq20161117-SAM-Ind25.png|Right-most aligned reads in SAM format | |||
</gallery> | |||
Once again, base qualities are generally poor and the matching region for the aligned bp does not leave the AmpF region. So this isn't helpful. |
Revision as of 21:06, 21 November 2016
Sequencing Results-Miseq 2016-11-17
Circularization Optimization Testing (Started Oct 31)
This was a repeat of the sequencing from 11-10, for which the results are analyzed on Daniel:Notebook/ComboLock/2016-11-18) The base qualities and results were not great, so I tried to repeat it. However, we can see:
- Miseq20161117-BaseQual-Ind30.png
Base qualities for index 30
- Miseq20161117-BaseQual-Ind31.png
Base qualities for index 31
- Miseq20111117-SAM-Ind30.png
SAM results for index 30
- Miseq20161117-SAM-Ind31.png
SAM results for index 31
that the base qualities are all poor. Further, of the few sequences that actually aligned to the template, none of them are sufficiently out of the AmpF region (approximately bp 56). To make this calculation you can take the alignment position in column 4 and compare it against the number of matches in the CIGAR string (column 6) and see that 59 is about as high as it gets, which isn't necessarily far enough into the next region to determine its identity.
Cell Test with RCA (Started Nov 7)
Unfortunately, this winds up to the same problems as above. See the gallery below.
- Miseq20161117-BaseQual-Ind25.png
Base qualities
- Miseq20161117-SAM-Ind25.png
Right-most aligned reads in SAM format
Once again, base qualities are generally poor and the matching region for the aligned bp does not leave the AmpF region. So this isn't helpful.