Open my alignment in Tablet

[Guigra]

Hi,

I'm trying to open my alignment in the Tablet, but is taking too long. My alignment is in sam format, and has about 11GB. Convert the file to bam format, but is taking too long. Anyone know a faster program to view my alignments?

Tanks!

[mastal]

Open my alignment in Tablet

Try Hawkeye.

[maubp]

Tablet will load SAM files but it is far far faster and more memory efficient to use BAM instead.

Any large SAM file is best converted to BAM as early as possible - it will be smaller for a start, and then it can be indexed for efficient random access. It will take a while, but it will make later tasks faster (or possible).

[Guigra]

But ever I try open my alignment im bam format, the tablet give me this mensage:

"An error has occurred whiele attempting to open trovide assembly. java.ioIOException: An index file could not be found. You may need to use samtools to generate one."
How I do this index?

[maubp]

A quick search should have answered that. At the command line, using samtools:

samtools index example.bam

This will create an index file with the extension .bai which is used for any analysis requiring random access to the BAM file based on coordinates. This is essential for Tablet or any other BAM viewing software.

[Guigra]

Thank you, your tip was very valuable. I managed to open my alignment very fast, it was very useful!