diff --git a/docs/next_gen.sgml b/docs/next_gen.sgml index ebdb54742c59146852c054e78259f6c4e1f3d76e..683c6d06bd2ace4fb2eacd985530506d16e80372 100644 --- a/docs/next_gen.sgml +++ b/docs/next_gen.sgml @@ -17,7 +17,7 @@ path names to the BAM files. The BAM files can be read from a local file system from an HTTP server. </PARA> <PARA> -BamView will look to match the length of the sequence in Artemis with the reference sequence lengths +BamView will look to match the length of the sequence in &prog; with the reference sequence lengths in the BAM file header. It will display a warning when it opens if it finds a matching reference sequence (from these lengths) and changes to displaying the reads for that. The reference sequence for the mapped reads can be changed manually in the drop down list in the toolbar at the top of the BamView. @@ -25,7 +25,7 @@ reads can be changed manually in the drop down list in the toolbar at the top of <PARA> In the case when the reference sequences are concatenated together into one (e.g. in a multiple FASTA sequence) and the sequence length matches the sum of sequence lengths given in the -header of the BAM, Artemis will try to match the names (e.g. locus_tag or label) of the +header of the BAM, &prog; will try to match the names (e.g. locus_tag or label) of the features (e.g. contig or chromosome) against the reference sequence names in the BAM. It will then adjust the read positions accordingly using the start position of the feature. </PARA> @@ -35,7 +35,7 @@ BamView panel. The 'View' menu allows the reads to be displayed in a number of v strand-stack, paired-stack, inferred size and coverage. </PARA> <PARA> -In Artemis the BamView display can be used to calculate the number of reads mapped to the +In &prog; the BamView display can be used to calculate the number of reads mapped to the regions covered by selected features. In addition the reads per kilobase per million mapped reads (RPKM) values for selected features can be calculated on the fly. Note this calculation can take a while to complete.