MinION Coverage sensitivity analysis - Revision history

Rf: s2

2017-04-09T12:23:34Z

Rf: s2

2017-04-09T12:05:22Z

Rf at 17:24, 7 April 2017

2017-04-07T17:24:41Z

Rf: Created page with " = Subtract Operations = In the spirit of discovering new sequences, this ivolves subtract what is currently annotated from our alignment dataset. This is a highly untarget..."

2017-03-28T17:16:31Z

Created page with " = Subtract Operations = In the spirit of discovering new sequences, this ivolves subtract what is currently annotated from our alignment dataset. This is a highly untarget..."

New page

= Subtract Operations =

In the spirit of discovering new sequences, this ivolves subtract what is currently annotated from our alignment dataset.

This is a highly untargeted approach because all currently annotated genes and interestung areas are subtracted so that the coverage can only describe currently unknown areas of the genome, including non-coding areas.

Though this might sound unfruitful to start with, it has some benefits:
* useful to gain a feeling of general coverage
* reduces reliance on currently known areas, which may have been chosen becaus eof high coverage from previous studies.

= Intersect Operations =

@@ Line 11: / Line 11: @@
 = Conversion of base-called fast5 to fasta=
-This is done with poretools, and can be performed. Filters may be
+This is done with <code>poretools</code>, and can be performed. Filters for minimum read length can be employed. The average read lenght on this experiment was 4000 bp, so it was decided to use two filters, one for 1kbp and another for 2kbp. Two values would help see how valuable stringency on read length could be.
 = Subtract Operations =
-In the spirit of discovering new sequences, this ivolves subtract what is currently annotated from our alignment dataset.
+In the spirit of discovering new sequences, this involves subtracting what is currently annotated from our alignment dataset.
 This is a highly untargeted approach because all currently annotated genes and interestung areas are subtracted so that the coverage can only describe currently unknown areas of the genome, including non-coding areas.
@@ Line 26: / Line 37: @@
 = Intersect Operations =
 = Obtaining the sequence behind a range =
-As the bed file only holds chromosome names and ranges, there is no sequence information. This is obtain with the bedtools getfasta tool. This however needs a fasta file, so the correct fasta must be obtained from the bam file, because the reference sequence could be used or sequences from the reads.
+As the bed file only holds chromosome names and ranges, there is no sequence information. This is obtained with the bedtools getfasta tool. This however needs a fasta file, so the correct fasta must be obtained from the bam file, because the reference sequence could be used or sequences from the reads.

← Older revision		Revision as of 12:05, 9 April 2017
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		+	= Introduction =

		+	MinION is a new (at time of writing, 2017) sequencing technology capable of very long reads (sometimes, 30kbp).

		+	Due to its lower maturity compared to other technologies, such as Illumina, it also is less robust, leading to scenarios where quality can be too low. In Illumina, such reads are usually discarded, but it in MinION it is less easy to make that decision, because:
		+	* longer reads inherently more valuable due to their ability to span long genomic regions
		+	* too high a quality threshold may discard the majority of reads
		+
		+	While retaining low quality sequencing is not usually a merit of an experiment where high quality reads are in abundance, it is beneficial to at least accompany these with a sensivity analysis which may help extract the usefulness of such reads.

	= Conversion of base-called fast5 to fasta=		= Conversion of base-called fast5 to fasta=

← Older revision		Revision as of 17:24, 7 April 2017
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		+
		+
		+
		+	= Conversion of base-called fast5 to fasta=
		+
		+	This is done with poretools, and can be performed. Filters may be


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	= Intersect Operations =		= Intersect Operations =
		+
		+
		+	= Obtaining the sequence behind a range =
		+
		+	As the bed file only holds chromosome names and ranges, there is no sequence information. This is obtain with the bedtools getfasta tool. This however needs a fasta file, so the correct fasta must be obtained from the bam file, because the reference sequence could be used or sequences from the reads.