Manipulating .sam files

[anunn]

Hi Guys,

I want to do something very simple, but I'm finding it very difficult to make any headway.

I have .sam files from a sequencing experiment, and I want to visualise a few small regions by uploading them to UCSC. The problem is, I can't even open a .sam file let alone select specific information.

I can't seem to open the .sam file in MySQL Workbench - is this even the right program to use?

I suppose the question I'm asking is, what is the *simplest* way of taking a 4GB .sam file, and extracting the reads that align to say, Chr1, and saving them as a new .sam file?

Many thanks!

Adam

[colindaven]

Try Tablet, it's very good. You'll need the reference sequence, and the chromosome of the reference sequence you use should exactly match that in the SAM file.

To look at your SAM file try the Large Text File Viewer if you're using windows. If in Linux use the commands head or more.

I would stay well clear of Mysql workbench here.

And to answer your concrete question : I would use the "grep" command to filter chr1 sequences on a Linux (or, I think, Mac) system. On Windows I don't know!

You can also try SAM-> BAM conversion using Picard.

[ttnguyen]

Also try SeqMonk http://www.bioinformatics.bbsrc.ac.uk/projects/seqmonk/
This java-based tool is OS independent.

[krobison]

SAM files are not MySQL files.

samtools are a good basic tool for this. Not only can you pull out a chromosome, but also specify a specific region

Your new SAM file may not be usable by anything downstream if you aren't careful with grep (you need to make sure the header comes along), but that doesn't mean I don't trod that thin ice routinely!