Getting back on tracks

Posted by & filed under Panopea generosa.

Yesterday I uploaded v0.0.1 of the Geoduck genome to CoGe. Now I want to start adding tracks. To do this I used CLC to create RNA-seq tracks from our male and female gonad transcriptome data. As would be expected only a small amount of reads mapped. This is as we are limiting the genome to… Read more »

Passing Flanks

Posted by & filed under Ostrea lurida.

A first look at population differences at qPCR primer sites for three population of Olympia oysters Plate 1 (samwhite_112381) included, BMP2, CARM, HSPb11, and PGEEP4. At the bottom is a full list of qPCR primers. BMP2 Limited coverage CARM Better coverage conflicts were ambigs (ie S,W,R) HSPb11 Missed qPCR primer (R did not seem to… Read more »

Quick Carmalign

Posted by & filed under Ostrea lurida.

The first batch of sequencing came into today to verify sequence of Olympia oyster qPCR primers. 1) imported .ab1 files into CLC, 2) trimmed “CARM” sequences 3) aligned to comp7220_c0_seq2

Wayback to just-MBD

Posted by & filed under Cgigas DNA Methylation.

Prior to bisulfite sequencing we did do a couple of MBD enrichment libraries to describe DNA methylation in oysters. Results even were snuck into this perspective. While I am sure there are genome tracks around, I am ending up #doingitagain. In short I took the raw Solid reads, align to Crassostrea_gigas.GCA_000297895.1.26.dna.genome in CLC, exported bam,… Read more »