-back to CLC
s7=control and s6=Laby. I had to tape a post it note to my computer so I'd remember.
^file structure
-----
raw
s7 34.330.892
s6 36.887.726
after trim
s7 34.269.810
s6 36.774.738
-
Trimmed sequences were then de novod
=--
annotated contigs with SP
going to put top hit SP ID into DAVID
Back at trying to make pie chart from GO slims of simple de novo
^for this table each feature has a corresponding GOSlim term only once.
without OTHERs
^corresponding Excel File.
Lets get a short list of cool genes from denovo
2045 unique contigs were with "stress response" as GOslim term
^
does not show
| response to DNA damage stimulus |
956 |
| DNA repair |
938 |
| response to stress |
576 |
or
| defense response to fungus |
2 |
| DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis |
2 |
| DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator |
2 |
| double-strand break repair via homologous recombination |
2 |
| hemolymph coagulation |
2 |
| natural killer cell mediated cytotoxicity |
2 |
| response to cold |
2 |
| activation of JUN kinase activity |
1 |
| behavioral fear response |
1 |
| cellular response to glucose starvation |
1 |
| cellular response to heat |
1 |
| DNA ligation during DNA repair |
1 |
| evasion by virus of host immune response |
1 |
| G1/S DNA damage checkpoint |
1 |
| intra-S DNA damage checkpoint |
1 |
| JNK cascade |
1 |
| nucleotide-excision repair |
1 |
| nucleotide-excision repair, DNA duplex unwinding |
1 |
| nucleotide-excision repair, DNA incision |
1 |
| nucleotide-excision repair, DNA incision, 3'-to lesion |
1 |
| nucleotide-excision repair, DNA incision, 5'-to lesion |
1 |
| positive regulation of JUN kinase activity |
1 |
| postreplication repair |
1 |
| regulation of DNA repair |
1 |
| regulation of JNK cascade |
1 |
| response to endoplasmic reticulum stress |
1 |
| response to hydrogen peroxide |
1 |
| response to pain |
1 |
Going to run some assembly stats / graphics
Graphics not that interesting
SPSS file
RNAseq
Methods
46 genes were only expressed in Laby library
(note have minimally 15 hits)
78 only in control
(note have at min 14 hits)
270 greater than 4 fold in Laby
255 greater than 4 fold in Control
--
503 total p value less than .05
of those there were 215 SPIDs
235 up in Laby
268 up in control
There are a total of 90 with associated GO slim terms for BP
--
31357 unique SPID in total 90230 contigs
--
^contains SPID for de novo, 4+folders, and pvalued.
#fail made some typos and figures are not accurate.
DAVID
on FULL DENOVO
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-1.png)
-2.png)
-3.png)
;%20Science%20Applications%20International%20Corporation%20(SAIC).png)