SequencingFormats - Revision history

Sgupta at 16:03, 4 November 2019

2019-11-04T16:03:21Z

2019-11-04T16:03:15Z

2018-01-24T19:33:23Z

2018-01-24T19:33:01Z

2018-01-24T19:32:42Z

2017-11-08T15:25:30Z

2017-01-12T20:16:55Z

2017-01-12T20:07:05Z

2016-05-17T18:01:53Z

2016-05-17T17:53:06Z

← Older revision		Revision as of 16:03, 4 November 2019
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	We typically provide the following files/formats as part of a typical data package for HiSeq Sequencing Data. Base calls were performed by the instrument control software and further processed using the Offline Base Caller (Illumina) v. 1.9.4. Quality control/assessment was performed using fastqc, fastqscreen and custom scripts.		We typically provide the following files/formats as part of a typical data package for HiSeq Sequencing Data. Base calls were performed by the instrument control software and further processed using the Offline Base Caller (Illumina) v. 1.9.4. Quality control/assessment was performed using fastqc, fastqscreen and custom scripts.
−

	<b>WE SPIKE (less than 3%) PHIX IN EVERY LANE. PhIX data along with any reads that could not be demultiplexed are moved in unknown-s_<lane>_<read>_sequence.txt file.</b>		<b>WE SPIKE (less than 3%) PHIX IN EVERY LANE. PhIX data along with any reads that could not be demultiplexed are moved in unknown-s_<lane>_<read>_sequence.txt file.</b>

← Older revision		Revision as of 16:03, 4 November 2019
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−	We typically provide the following files/formats as part of a typical data package for HiSeq ~~as well as Genome Analyzer~~ Sequencing Data.	+	We typically provide the following files/formats as part of a typical data package for HiSeq Sequencing Data. Base calls were performed by the instrument control software and further processed using the Offline Base Caller (Illumina) v. 1.9.4. Quality control/assessment was performed using fastqc, fastqscreen and custom scripts.
		+

	<b>WE SPIKE (less than 3%) PHIX IN EVERY LANE. PhIX data along with any reads that could not be demultiplexed are moved in unknown-s_<lane>_<read>_sequence.txt file.</b>		<b>WE SPIKE (less than 3%) PHIX IN EVERY LANE. PhIX data along with any reads that could not be demultiplexed are moved in unknown-s_<lane>_<read>_sequence.txt file.</b>

@@ Line 5: / Line 5: @@
 The directory structure for dataset handed over:
-[[image:seqdatapackage.png]]
+[[image:seqdatapackage.PNG]]
 == FASTQ Files (Quality Score Files) ==

@@ Line 5: / Line 5: @@
 The directory structure for dataset handed over:
-[[image:seqdataformat.jpg]]
+[[image:seqdatapackage.png]]
 == FASTQ Files (Quality Score Files) ==

@@ Line 5: / Line 5: @@
 The directory structure for dataset handed over:
-[[image:DataDirectoryStructure-Sequencing.jpg]]
+[[image:seqdataformat.jpg]]
 == FASTQ Files (Quality Score Files) ==

@@ Line 62: / Line 62: @@
 == FASTQ SCREEN Reports ==
-Each FASTQ file goes through our pipeline that generates FASTQ SCREEN reports. These will be handed over with the datasets starting 1st July 2016.
+Each FASTQ file goes through our pipeline that generates FASTQ SCREEN reports. These will be handed over with the datasets starting 1st November 2017.
 Please refer to the [http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/| FASTQ SCREEN Website] for details.

@@ Line 1: / Line 1: @@
 We typically provide the following files/formats as part of a typical data package for HiSeq as well as Genome Analyzer Sequencing Data.
-<b>WE SPIKE PHIX IN EVERY LANE AND ASSUME THE DE-MULTIPLEXING PROCESS REMOVES IT FROM THE ACTUAL LIBRARY DATA.</b>
+<b>WE SPIKE (less than 3%) PHIX IN EVERY LANE. PhIX data along with any reads that could not be demultiplexed are moved in unknown-s_<lane>_<read>_sequence.txt file.</b>
 The directory structure for dataset handed over:

← Older revision		Revision as of 20:07, 12 January 2017
Line 1:		Line 1:
	We typically provide the following files/formats as part of a typical data package for HiSeq as well as Genome Analyzer Sequencing Data.		We typically provide the following files/formats as part of a typical data package for HiSeq as well as Genome Analyzer Sequencing Data.
		+
		+	<b>WE SPIKE PHIX IN EVERY LANE AND ASSUME THE DE-MULTIPLEXING PROCESS REMOVES IT FROM THE ACTUAL LIBRARY DATA.</b>

	The directory structure for dataset handed over:		The directory structure for dataset handed over:

@@ Line 42: / Line 42: @@
 <pre>tar -xOzf xyz.tar.gz | gzip -f > xyz.fq.gz</pre>
@@ Line 48: / Line 49: @@
 Please refer to the [[SequencingQC|QC section]] for details.
 == FASTQC Reports ==
@@ Line 53: / Line 56: @@
 Please refer to the [http://www.bioinformatics.babraham.ac.uk/projects/fastqc/| FASTQC Website] for details.
 == FASTQ SCREEN Reports ==
@@ Line 58: / Line 63: @@
 Please refer to the [http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/| FASTQ SCREEN Website] for details.
 == laneannotation.xls ==
@@ Line 202: / Line 210: @@
 |Passed or Marginal or Failed Prep QC
 |}
 =Discontinued File Formats=

← Older revision		Revision as of 17:53, 17 May 2016
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	We typically provide the following files/formats as part of a typical data package for HiSeq as well as Genome Analyzer Sequencing Data.		We typically provide the following files/formats as part of a typical data package for HiSeq as well as Genome Analyzer Sequencing Data.
		+
		+	The directory structure for dataset handed over:
		+
		+	[[image:DataDirectoryStructure-Sequencing.jpg]]

	== FASTQ Files (Quality Score Files) ==		== FASTQ Files (Quality Score Files) ==