sensestrand.blogspot.com

The Sense Strand

A group blog for the Redfield lab to post their RNAseq analyses. Tuesday, July 21, 2015. New RNA-seq samples (quality). The new RNA-seq data arrived about a week and a half ago. Since then I've aligned it to the KW20 genome and looked a bit into the antitoxin knockout samples. But I wanted to mention the quality of the data. This analysis was done partially using FASTQC. Here are some interesting numbers:. Average # of reads of older samples: 7,643,000. Average # of reads of new samples: 11,620,000.

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The Sense Strand | sensestrand.blogspot.com Reviews

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A group blog for the Redfield lab to post their RNAseq analyses. Tuesday, July 21, 2015. New RNA-seq samples (quality). The new RNA-seq data arrived about a week and a half ago. Since then I've aligned it to the KW20 genome and looked a bit into the antitoxin knockout samples. But I wanted to mention the quality of the data. This analysis was done partially using FASTQC. Here are some interesting numbers:. Average # of reads of older samples: 7,643,000. Average # of reads of new samples: 11,620,000.

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the sense strand,posted by,scott m,no comments,recent lab meeting,mure crystal structures,the second,m tuberculosis,rnaseq docs/scott/recombination,4 comments,has caat repeats,in crpx,has agcag repeats,has aact repeats,compare kw20,and finally,3 comments

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The Sense Strand | sensestrand.blogspot.com Reviews

https://sensestrand.blogspot.com

A group blog for the Redfield lab to post their RNAseq analyses. Tuesday, July 21, 2015. New RNA-seq samples (quality). The new RNA-seq data arrived about a week and a half ago. Since then I've aligned it to the KW20 genome and looked a bit into the antitoxin knockout samples. But I wanted to mention the quality of the data. This analysis was done partially using FASTQC. Here are some interesting numbers:. Average # of reads of older samples: 7,643,000. Average # of reads of new samples: 11,620,000.

INTERNAL PAGES

sensestrand.blogspot.com

1

The Sense Strand: January 2015

http://www.sensestrand.blogspot.com/2015_01_01_archive.html

A group blog for the Redfield lab to post their RNAseq analyses. Saturday, January 24, 2015. I was looking at the BAM files I produced from the sequencing to verify all the strain had the genotype expected of them. Most of them did, but there was anissue with the supposed “cyaA” strain. Looking at the fastq files for these comN knockout samples, I've discovered reads for a spectinomycin cassette similar to this one:. In summary, there must have been some mix up at some point between the antitoxin knockou...

2

The Sense Strand: Things worth mentioning about competence genes in competence mutants

http://www.sensestrand.blogspot.com/2015/06/things-worth-mentioning-about.html

A group blog for the Redfield lab to post their RNAseq analyses. Monday, June 1, 2015. Things worth mentioning about competence genes in competence mutants. I've turned my focus on trying to figure out how/why the various competence mutants we have alter regular competence. To do this, I'm comparing expression of competence genes between strains. A quick message about normalization:. To make comparisons between genes possible, instead of asking "how much expression of gene A is there? The toxin and doubl...

3

The Sense Strand: July 2015

http://www.sensestrand.blogspot.com/2015_07_01_archive.html

A group blog for the Redfield lab to post their RNAseq analyses. Tuesday, July 21, 2015. New RNA-seq samples (quality). The new RNA-seq data arrived about a week and a half ago. Since then I've aligned it to the KW20 genome and looked a bit into the antitoxin knockout samples. But I wanted to mention the quality of the data. This analysis was done partially using FASTQC. Here are some interesting numbers:. Average # of reads of older samples: 7,643,000. Average # of reads of new samples: 11,620,000.

4

The Sense Strand: List of CRP-regulated genes

http://www.sensestrand.blogspot.com/2015/06/list-of-crp-regulated-genes.html

A group blog for the Redfield lab to post their RNAseq analyses. Monday, June 1, 2015. List of CRP-regulated genes. This data was produced by comparing the CRP knockout strain to KW20 in MIV only. This is based on one crpx timecourse replicate (I believe another replicate has been sent for sequencing). First I compiled a list of predicted CRP binding sites and associated them with genes predicted to be first in an operon (using data from DOOR. I uploaded the results to the Google Drive:.

5

The Sense Strand: April 2015

http://www.sensestrand.blogspot.com/2015_04_01_archive.html

A group blog for the Redfield lab to post their RNAseq analyses. Thursday, April 23, 2015. Ribosomal RNA in the RNA-seq samples. To get an estimate of the amount of ribosomal RNA in each sample, I took all the FASTQ files and aligned them to a FASTA file which contains all of the rRNA genes in Haemophilus influenzae. KW20 (which can be found here. Then I just looked to see what percentage of the reads aligned to these regions:. Antx M0 A 0.07%. Antx M1 A 0.06%. Antx M2 A 0.06%. Antx M3 A 0.07%. Sxyx M0 D...

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The Sense Strand

A group blog for the Redfield lab to post their RNAseq analyses. Tuesday, July 21, 2015. New RNA-seq samples (quality). The new RNA-seq data arrived about a week and a half ago. Since then I've aligned it to the KW20 genome and looked a bit into the antitoxin knockout samples. But I wanted to mention the quality of the data. This analysis was done partially using FASTQC. Here are some interesting numbers:. Average # of reads of older samples: 7,643,000. Average # of reads of new samples: 11,620,000.

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