[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

[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]

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]

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]

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, I missed one slash in the url.

The correct url is

http://qyz03/misc/test.bam

And now I see another problem. After loading the bam file, I concatenated all fasta files of human genome into hg18.fa and try uploding and I see the following error message.

Unfortunately, Tablet no longer has enough memory to complete its current task and must be closed.

[imilne]

Thank you so much Iain for your help. I have missed something in the url and now I am able to load.

Was it just simply a wrong URL? I'll need to check what Tablet is doing if that happens as that wasn't exactly the world's best error message for such a simple mistake

[seq_GA]

Thank you so much Iain for your help. I have missed something in the url and now I am able to load.

[imilne]

Check that your web browser will attempt to download the file if you paste the URL in that.

And also attach a copy of the "output.log" file from Tablet's install dir. It might give me a clue as to what's going wrong.

Iain

[seq_GA]

Hi Iain,

When I try pasting the below url as http:/qyz03/misc/test.bam in the primary assembly file or URL, the Reference/consensus file or URL becomes inactive and when I click open button, I get to see the following error:

An error has occurred while attempting to open the provided assembly. 
java.lang.NullPointerException

Input file(s) used:
http:/qyz03/misc/test.bam

How to overcome this? Sorry for asking too many questions. Thanks.

[seq_GA]

Thx Iain..

[imilne]

we have the bam files on a web server running on linux box. How to use Tablet in that case.

Just get the URL of the file on the clipboard (eg http://someserver/somefile.bam) and paste that into the Open Assembly dialog within Tablet. Same with the reference data if it's on the server too.

Iain

[seq_GA]

Thx Ian for the help. I will definitely try.
we have the bam files on a web server running on linux box. How to use Tablet in that case. I am downloading the windows version to try the next step. Thanks.

[imilne]

If you can network map to the BAM files from your windows desktop (or put the files on a web server running on the linux box), then it won't really matter. Tablet (and any of the graphical viewers) will let you look at the BAM file without having to copy the whole thing to your local system.

Iain

[seq_GA]

Hi all,
Thx for the response. Since I don't want to import bam files from the server into my desktop every time, I am working on making xwin32 to work..Thx again.