[imilne]

Yes, any reference data isn't disk cached yet so if you have a lot of it, you're going to need more memory. See http://bioinf.scri.ac.uk/tablet/help/memory.shtml if you need to allocate more (Tablet only asks for 1GB by default).

Iain

[seq_GA]

Yes, any reference data isn't disk cached yet so if you have a lot of it, you're going to need more memory. See http://bioinf.scri.ac.uk/tablet/help/memory.shtml if you need to allocate more (Tablet only asks for 1GB by default).

Iain

Hi Iain,

Do I need to change the setting tablet.vmoptions? How much should I increase? My PC has around 3.49G of RAM. Please let me know as I am not sure. Thanks.

[imilne]

Do I need to change the setting tablet.vmoptions? How much should I increase? My PC has around 3.49G of RAM.

Yep, you need to edit that file (when Tablet isn't running) and change the value to however much memory you want, but be aware that 32bit Windows probably won't be able to give you more than about 1500MB anyway. Ultimately it might be easier to chop your reference data into smaller pieces, say 1 or 2 chromosomes per file.

Iain

[seq_GA]

Ok. Iain, just for testing I just loaded chr10.fa and tablet shows 0 reads from the bam file. I am sure the bam file contains reads (pair end) from chr10.fa. The naming convention is also consistent like chr10 in bam as well as my reference genome starting >chr10. Why none of the reads are displayed. I assumed that even though the bam contains reads from all the chromosomes, I will get to see only reads from chr10. Or do I have to grep for only chr10 into a separate bam file and then upload? Please suggest me on how to proceed. Thanks.

[imilne]

Ok. Iain, just for testing I just loaded chr10.fa and tablet shows 0 reads from the bam file. I am sure the bam file contains reads (pair end) from chr10.fa. The naming convention is also consistent like chr10 in bam as well as my reference genome starting >chr10. Why none of the reads are displayed. I assumed that even though the bam contains reads from all the chromosomes, I will get to see only reads from chr10. Or do I have to grep for only chr10 into a separate bam file and then upload? Please suggest me on how to proceed. Thanks.

(This is something that's been improved in the latest development Tablet)

I'm assuming you're seeing 0 because you haven't actually looked at the contig yet? We're not aware of a method of querying a BAM file that will tell us how many reads are in a contig, without actually having to load a block of data. So until you start looking at it, that number will be 0. Once you load a region, and there's reads in that region (no guarantee there either), then the number will change.

Iain