Editing
Alice:Exome Sequencing Analysis/analysis pipeline
(section)
Jump to navigation
Jump to search
Warning:
You are not logged in. Your IP address will be publicly visible if you make any edits. If you
log in
or
create an account
, your edits will be attributed to your username, along with other benefits.
Anti-spam check. Do
not
fill this in!
===Generate data annotation file (.info file)=== * First, generate a text file containing your data information. This file should look like the following: genome-miner 1 exome SampleID LibraryID FlowCell Lane Barcode File1 File2 CV-iF AL-Exome-CV-iF-PP HL022 s5 NA /media/Syn_15T/Ext9T_Backup/SeqStore2009/091109_HL022/s_5_sequence.txt.gz CV-iF AL-Exome-CV-iF-PP HL022 s6 NA /media/Syn_15T/Ext9T_Backup/SeqStore2009/091109_HL022/s_6_sequence.txt.gz CV-iF AL-Exome-CV-iF-PP HL022 s7 NA /media/Syn_15T/Ext9T_Backup/SeqStore2009/091109_HL022/s_7_sequence.txt.gz CV-iF AL-Exome-CV-iF-PP HL025 s7 NA /media/Syn_15T/Ext9T_Backup/SeqStore2009/091123_HL025/s_7_sequence.txt.gz CV-iF AL-Exome-CV-iF-PP HL026 s5 NA /media/Syn_15T/Ext9T_Backup/SeqStore2009/091127_HL026/s_5_sequence.txt.gz CV-iF AL-Exome-CV-iF-NG HL053 s2 NA /media/SeqStore2/100503_HL053/s_2_1_sequence.txt.gz /media/SeqStore2/100503_HL053/s_2_2_sequence.txt.gz * This file is a tab-delimited text file containing 7 columns * The first three lines list script parameters. ** Line 1: Please write either "genome-miner" or "tscc" based on the system of choice ** Line 2: Please write "1" to remove clonal reads or "0" to keep clonal reads ** Line 3: Please write "exome" to limit realignment and variant calling to coding regions, or "genome" to look at all regions ** Line 4: MUST contain the header line listed above. * Each line represents one SE fastq file or a pair of PE fastq files. * Detailed description of each column: ** Column 1: SampleID *** This column should contain a short identifier describing your sample(s). *** If multiple samples are provided, a multi-sample BAM file will be generated and multi-sample variant calling will be performed. ** Column 2: LibraryID *** This column should describe details of your library. *** Generally, you should include the initials of the person making the library, the type (Exome, Genome, BSPP, etc), and the sampleID. *** If you generated multiple sequencing libraries for your samples, please provide them unique identifiers here to facilitate proper removal of clonal reads *** For example, here I have denoted that one library was made using padlock probes and one was made using NimbleGen Exome Capture. ** Column 3: FlowCell *** This column should contain the flow cell in which the fastq file was sequenced. ** Column 4: Lane *** This column should contain the letter "s" followed by the lane number. ** Column 5: Barcode *** This column should list the barcode used for the library. *** Examples: "NA" for no barcode or "Indx7" for barcode #7, etc. ** Column 6: First End FASTQ file *** This file should list the full path to the first end FASTQ file. *** For Single-End data, simply provide the path to the FASTQ file. ** Column 7: Second End FASTQ File *** This column should list the full path to the second end FASTQ file *** For single-end data, this column should be left blank. * Save this file with a .info extension. I will call the file "prefix.info" in this example. * Upload this file to genome-miner to your folder of choice. For this example, we will use /home/ajgore/TestRun.
Summary:
Please note that all contributions to ZhangLabWiki may be edited, altered, or removed by other contributors. If you do not want your writing to be edited mercilessly, then do not submit it here.
You are also promising us that you wrote this yourself, or copied it from a public domain or similar free resource (see
ZhangLabWiki:Copyrights
for details).
Do not submit copyrighted work without permission!
Cancel
Editing help
(opens in new window)
Navigation menu
Personal tools
Not logged in
Talk
Contributions
Create account
Log in
Namespaces
Page
Discussion
English
Views
Read
Edit
View history
More
Search
Navigation
Main Page
Current events
Recent changes
Random page
Investigators
Matt Cai
Song Chen
Eric Chu
Dinh Diep
Elizabeth Duong
Shicheng Guo
Alan Fung
Daniel Jacobsen
Blue Lake
Huy Lam
Alice Li
Andrew Richards
Brandon Sos
Chris Wei
Yan Wu
Kun Zhang
Tools
What links here
Related changes
Special pages
Page information