JP Jan 21 16 - Revision history

Jupreziosi at 19:50, 21 January 2016

2016-01-21T19:50:57Z

Jupreziosi at 19:47, 21 January 2016

2016-01-21T19:47:40Z

Jupreziosi at 19:41, 21 January 2016

2016-01-21T19:41:14Z

Jupreziosi at 19:35, 21 January 2016

2016-01-21T19:35:48Z

Jupreziosi at 19:35, 21 January 2016

2016-01-21T19:35:38Z

Jupreziosi at 19:34, 21 January 2016

2016-01-21T19:34:46Z

Jupreziosi at 19:05, 21 January 2016

2016-01-21T19:05:37Z

Jupreziosi: Created page with "'''Looking at reports downloaded 1-19-16''' split_1no_i.fastq, etc No = not fed i = intestine Left: green check = good; orange ! = suspect; red X = something wrong. Per ba..."

2016-01-21T19:04:39Z

Created page with "'''Looking at reports downloaded 1-19-16''' split_1no_i.fastq, etc No = not fed i = intestine Left: green check = good; orange ! = suspect; red X = something wrong. Per ba..."

New page

'''Looking at reports downloaded 1-19-16'''

split_1no_i.fastq, etc
No = not fed
i = intestine

Left: green check = good; orange ! = suspect; red X = something wrong.

Per base sequence quality
40 = perfect score for each base. Unsure bases get lower scores.
>= 20 is good.

Per tile sequence quality
cDNA all sequenced at once. Positions on the chip where sequences were read.

Per sequence quality scores
A few reads below 30, but more sequences had quality around 38.

Per base sequence content
First few bases are the bar codes.
Each set of sequences has its own bar code (ex 1_i = AGG, 2_i = CGG)
The bar codes aren't a part of the RNA sequence; they need to be removed from any analysis.
Trim off the first 4; if any are scored below 15, they will be thrown away; sequences that are less than 30bp left are thrown out of analysis.

Per sequence GC content
intestines' content all closely match the theoretical distribution. Liver has multiple peaks of distribution. Maybe this is biological and not data error.

Per base N content
Almost 0 n; program was able to determine bases.

Sequence Length Distribution
About 76 bp

Sequence Duplication Levels
Unclear how to translate this. Deduplicated sequence? Almost all the reads are single copy (1 - 85). Might change when we delete bar codes.

Overrepresented sequences
Some samples have more than others.
* want to blast them ourselves

Kmer Content
Repeat units at very early positions; could go to zero when bar codes are eliminated.

← Older revision		Revision as of 19:50, 21 January 2016
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		+	[[Julia Preziosi]]
		+
	'''Looking at reports downloaded 1-19-16'''		'''Looking at reports downloaded 1-19-16'''

← Older revision		Revision as of 19:47, 21 January 2016
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	"an R-script was used to filter and count the number of genes that were significantly differentially expressed in individual tissues or in all tissues in multi-tissue comparisons" (10).		"an R-script was used to filter and count the number of genes that were significantly differentially expressed in individual tissues or in all tissues in multi-tissue comparisons" (10).
		+
		+	Sup Table S10; it would be interesting to see how our numbers of differentially expressed genes shared between samples compare to theirs; since we have a shorter time frame, we will probably have less genes. 0-.5 hrs instead of 0-24 hrs.

← Older revision		Revision as of 19:41, 21 January 2016
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	'''Supplementary Information'''		'''Supplementary Information'''
		+
		+
		+	"The final assembly resulted in 759,403 contigs, with a contig N50 size of 10,203 bp, and a total contig length of 1.4440 Gbp. The scaffold N50 for this assembly was 201,400 bp" (2)
		+
		+	'The N50 length is defined as the length for which the collection of all contigs of that length or longer contains at least half of the sum of the lengths of all contigs, and for which the collection of all contigs of that length or shorter also contains at least half of the sum of the lengths of all contigs.' (Google search)
		+
		+	Scaffold - putting together contigs with known lengths between them.
		+
		+	"25,385 genes" (3).
		+
		+	"Total RNA was extracted using Trizol Reagent (Invitrogen), following the manufacturer’s protocol. Illumina mRNAseq barcoded libraries were constructed with the Illumina TruSeq RNAseq kit and protocol. Total RNA and mRNA was quality-checked using a BioAnalyzer RNA 6000 pico chip (Agilent). Completed libraries were quantified and checked for appropriate size distribution using the DNA 7500 nono chip on a BioAnalyzer (Agilent)" (9).
		+
		+	"an R-script was used to filter and count the number of genes that were significantly differentially expressed in individual tissues or in all tissues in multi-tissue comparisons" (10).

← Older revision		Revision as of 19:35, 21 January 2016
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−	~~"""~~Supplementary Information~~"""~~	+	'''Supplementary Information'''

← Older revision		Revision as of 19:35, 21 January 2016
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	"The annotated genome assembly is available under the National Center for Biotechnology Information Bioproject PRJNA61234 (GenBank ac- cession no. AEQU00000000)" (6).		"The annotated genome assembly is available under the National Center for Biotechnology Information Bioproject PRJNA61234 (GenBank ac- cession no. AEQU00000000)" (6).
		+
		+
		+
		+	"""Supplementary Information"""

@@ Line 51: / Line 51: @@
 Kmer Content
 Repeat units at very early positions; could go to zero when bar codes are eliminated.
 ----
 '''The Burmese python genome reveals the molecular basis for extreme adaptation in snakes'''

← Older revision		Revision as of 19:05, 21 January 2016
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	Kmer Content		Kmer Content
	Repeat units at very early positions; could go to zero when bar codes are eliminated.		Repeat units at very early positions; could go to zero when bar codes are eliminated.
		+
		+
		+	----
		+
		+	'''The Burmese python genome reveals the molecular basis for extreme adaptation in snakes'''