Also, I wanted to know how many of the contigs with microsatellites were annotated and made the notebook
https://github.com/sr320/paper-pano-go/blob/master/jupyter-nbs/14Panopea_msat.ipynb
and I don't know why I couldn't merge the microsatellite file with the bigtable V08. so I only obtained the annotated microsatellites (I didn't want to expend more time), and found 130 annotated contigs with micros (check Out[9]). of those the motifs were
motif
count
AAG
2
AC
24
ACC
1
AG
24
AT
78
ATC
1
and only three were over expressed in females
sex-based_expresssion
count
female
2
female>male
1
contig
sex-based
gene
comp140811_c0_seq2
female
Oxalate:formate antiporter (OFA) (Oxalate:formate antiport p
comp137592_c0_seq4
female
Photoreceptor-specific nuclear receptor (Nuclear receptor su
I was thinking just mention the total number (130) of microsatellite that were annotated, and their motif counts, but without mentioning sex-based_expression.
Please let me know if what you think.
See you tomorrow? 9:00 or 11:00
@sr320 Hi Steven I have uploaded the microsatellite file https://github.com/sr320/paper-pano-go/blob/master/data-results/geoduck-v3microsatellites.csv and primers https://github.com/sr320/paper-pano-go/blob/master/data-results/geoduck-v3primers.csv
Also, I wanted to know how many of the contigs with microsatellites were annotated and made the notebook https://github.com/sr320/paper-pano-go/blob/master/jupyter-nbs/14Panopea_msat.ipynb and I don't know why I couldn't merge the microsatellite file with the bigtable V08. so I only obtained the annotated microsatellites (I didn't want to expend more time), and found 130 annotated contigs with micros (check Out[9]). of those the motifs were
and only three were over expressed in females
Note: the names are not complete.
It seems that the Oxalate:formate antiporter is bacterial (http://www.uniprot.org/uniprot/Q51330)! while "Photoreceptor-specific nuclear receptor. Transcriptional factor that is an activator of rod development and repressor of cone development" (http://www.uniprot.org/uniprot/Q9TTF0). and Transmembrane protein 178B is a Multi-pass membrane protein (http://www.uniprot.org/uniprot/H3BS89#subcellular_location) I don't know how to interpret these results.
I was thinking just mention the total number (130) of microsatellite that were annotated, and their motif counts, but without mentioning sex-based_expression. Please let me know if what you think. See you tomorrow? 9:00 or 11:00