Changes between Version 75 and Version 76 of SOPs/mapping


Ignore:
Timestamp:
03/25/22 11:39:13 (3 years ago)
Author:
thiruvil
Comment:

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  • SOPs/mapping

    v75 v76  
    130130
    131131The parameters included in the above sample command are:
    132   * '''--sjdbOverhang  ''' Specifies the length of the genomic sequence around the annotated junction to be used in constructing the splice junctions database.  For short reads (<50) use readLength - 1, otherwise a generic value of 100 will work as well for most long reads (see manual for more info and [[https://github.com/alexdobin/STAR/issues/551 | github response with reads longer than 100 bp]]).
     132  * '''--sjdbOverhang  ''' Specifies the length of the genomic sequence around the annotated junction to be used in constructing the splice junctions database.  For short reads (<50) use readLength - 1, otherwise a generic value of 100 will work as well for most long reads (see manual for more info and [[https://github.com/alexdobin/STAR/issues/551#issuecomment-458697789 | github response with reads longer than 100 bp]]).
    133133  * '''--sjdbGTFfile <GTF_file.gtf>''' Supplies STAR with a GTF file during the genomeGenerate step.  Combined with the --sjdbScore <n> option during mapping, this will bias the alignment toward annotated junctions, and reduces alignment to pseudogenes.
    134134  * '''--genomeSAindexNbases''' For small genomes, the parameter --genomeSAindexNbases must to be scaled down, with a typical value of min(14, log2(GenomeLength)/2 - 1).