Comments for Sam's Notebook

Comment on Genome Assembly – minimap/miniasm/racon Overview by tom

tom — Tue, 09 Apr 2019 18:37:58 +0000

In case somebody else finds this (like i did today) and despairs because it doesn’t work (like i did today):

I’m pretty sure there is an error in step 4. You don’t “map the fastq reads back to the contigs (the PAF file) created in the first step”. You instead map the fastq reads against the converted assembly from step 3.

The example given would suggest mapping the alignment map from step 1 against the assembly created in step 2. Which is not what the text says, but doesn’t look correct either.

Comment on Reverse Transcription – Ronit’s C.gigas DNased ctenidia RNA by qPCRs – Ronit’s C.gigas ploidy/dessication/heat stress cDNA (1:5 dilution) | Sam's Notebook

Thu, 18 Oct 2018 21:04:06 +0000

[…] The cDNA used for the qPCRs described below was a 1:5 dilution of Ronit’s cDNA made 20181017 with the following primers! Diluted cDNA was stored in his -20oC box with his original […]

Comment on DNase Treatment – Ronit’s C.gigas Ploiyd/Dessication Ctenidia RNA by Reverse Transcription – Ronit’s C.gigas DNased ctenidia RNA | Sam's Notebook

Wed, 17 Oct 2018 21:06:47 +0000

[…] Proceeded with reverse transcription of Ronit’s DNased ctenidia RNA (from 20181016). […]

Comment on gDNA Isolation – Mac’s BB and DH site samples by qPCR – Ronit’s DNAsed C.gigas Ploidy/Dessication RNA with elongation factor primers | Sam's Notebook

Wed, 17 Oct 2018 20:03:04 +0000

[…] BB16 from 20090519 was used as a positive control. […]

Comment on DNase Treatment – Ronit’s C.gigas Ploiyd/Dessication Ctenidia RNA by qPCR – Ronit’s DNAsed C.gigas Ploidy/Dessication RNA with elongation factor primers | Sam's Notebook

Wed, 17 Oct 2018 20:00:54 +0000

[…] DNA and primers to use to detect gDNA in Crassostrea gigas samples, I checked Ronit’s DNased RNA (from 20181016) for residual […]

Comment on qPCR – C.gigas primer and gDNA tests with 18s and EF1 primers by qPCR – Ronit’s DNAsed C.gigas Ploidy/Dessication RNA with elongation factor primers | Sam's Notebook

Wed, 17 Oct 2018 20:00:23 +0000

[…] After I figured out the appropriate DNA and primers to use to detect gDNA in Crassostrea gigas sampl…, I checked Ronit’s DNased RNA (from 20181016) for residual gDNA. […]

Comment on qPCR – C.gigas primer and gDNA tests with 18s and EF1 primers by Sam's Notebook

Sam's Notebook — Wed, 17 Oct 2018 19:59:11 +0000

[…] After I figured out the appropriate DNA and primers to use to detect gDNA in Crassostrea gigas sampl…, I checked Ronit’s DNased RNA (from 20181016) for residual gDNA. […]

Comment on gDNA Isolation – Mac’s BB and DH site samples by qPCR – C.gigas primer and gDNA tests with 18s and EF1 primers | Sam's Notebook

Wed, 17 Oct 2018 15:43:34 +0000

[…] addition to BB15 from 20090519, I decided to test out BB16 from 20090519 as a positive […]

Comment on DNase Treatment – Ronit’s C.gigas Ploiyd/Dessication Ctenidia RNA by qPCR – Ronit’s DNAsed C.gigas Ploidy/Dessication RNA with 18s primers | Sam's Notebook

Wed, 17 Oct 2018 15:26:34 +0000

[…] DNasing Ronit’s RNA earlier today, I needed to check for any residual […]

Comment on RNA Quantification – Ronit’s C.gigas Ploidy/Dessication RNA by DNase Treatment – Ronit’s C.gigas Ploiyd/Dessication Ctenidia RNA | Sam's Notebook

Tue, 16 Oct 2018 22:36:02 +0000

[…] quantifying Ronit’s RNA earlier today, I DNased them using the Turbo DNA-free Kit (Ambion), according to the manuacturer’s standard […]