如果序列文件的染色體名稱和你的Fasta文件和註釋文件不同時,需要建立名稱對應文件alias文件

創建對應文件的過程:

Creating a Chromosome Name Alias File

One of the common causes for a data loading failure is a mismatch in chromosome names between the data file and the IGV genome it is being viewed against.  Many Bowtie users report this problem after aligning to the supplied NCBI index files because chromosomes are named by accession numbers in the form: gi|224589811|ref|NC_000002.11|. 

The workaround is to create an alias file in 2-column tab-delimited format.  The first column contains the chromosome name in your data file, for example wig or bam file.  The second column contains the corresponding name in the genome assembly you are viewing (e.g., chr1 for our "hg19" genome).  For instance, the alias file might look like this:

NC_000002.11  <tab>  gi|224589811|ref|NC_000002.11|
NC_000002.12  <tab>  gi|224589811|ref|NC_000002.12|

Name the file after the genome with an underscore, the word "alias", and the extension .tab.  For example, hg19_alias.tab.  Place this file in the igv directory. The default location for this folder <user home>/igv/genomes, it can be changed in Preferences -> Advanced

Note: Certain well-known aliases are built into IGV and do not require an alias file.  These include mappings that involve adding or removing the prefix "chr" to the name, for example  1 -> chr1 and chr1 -> 1.    Also, NCBI identifiers that start with "gi|" and follow the pattern illustrated in the example above are automatically mapped. 

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