How do I create/find a bam index file for using the bamread function?
2 Ansichten (letzte 30 Tage)
Ältere Kommentare anzeigen
I use Galaxy to align DNA sequences with Bowtie. This produces a bam file which I can read with baminfo from the Bioinformatics toolbox, but not an index file. How do go about creating a proper index file to use with bamread? Thanks,
0 Kommentare
Akzeptierte Antwort
Razvan
am 10 Okt. 2012
You can use a BioMap object to load the information from the BAM file without the BAI file. See instructions here: http://www.mathworks.com/help/bioinfo/ug/storing-and-managing-short-read-sequence-data-in-objects.html
For example if you want to load the data from chromosome 1, you do this:
info = baminfo(bamFilename,'ScanDictionary',true);
bm = BioMap(bamFilename, 'SelectReference', 'ChrI');
Instead of 'ChrI' you can put any of the references that were used for mapping. These are stored here:
info.ScannedDictionary
The BioMap line will also generate a BAI file which you can use in bamread but that usually takes a lot more memory and it is slower.
Weitere Antworten (0)
Siehe auch
Kategorien
Mehr zu Data Import finden Sie in Help Center und File Exchange
Community Treasure Hunt
Find the treasures in MATLAB Central and discover how the community can help you!
Start Hunting!