Alex's BLAT recipe:
Downloading BLAT
To get BLAT source code:
$ mkdir /tmp/blat && cd /tmp/blat
$ wget http://hgwdev.cse.ucsc.edu/~kent/src/blatSrc.zip
$ unzip blatSrc.zip
Patching (optional)
I decided to make blat a static binary to avoid missing foo.so shared library errors. Here's a patch you can use to modify the blat makefile:
$ cat >> static-blat-makefile.patch
3c3
< L += -lm $(SOCKETLIB)
---
> L += -lm -ldl $(SOCKETLIB) -static-libgcc
10c10
< ${CC} ${COPT} ${CFLAGS} -o ${DESTDIR}${BINDIR}/blat $O $(MYLIBS) $L
---
> ${CC} ${COPT} ${CFLAGS} -o ${DESTDIR}${BINDIR}/blat $O -static $(MYLIBS) $L
You may need static library packages installed on your system. The names of these packages will depend on your version of Linux.
Then apply the patch:
$ cd /tmp/blat/blatSrc/blat
$ cp makefile makefile.original
$ patch makefile.original -i ../../static-blat-makefile.patch -o makefile
You may decide not to apply this patch. You could probably skip this step. I just don't like dynamic binaries.
Building BLAT
In any case, you will want to go to the top level of the blatSrc directory and run make to build the kit:
$ cd /tmp/blat/blatSrc && make
This will take a few minutes to build binaries.
Installing BLAT
To install them into ${HOME}/bin/${MACHTYPE}, run:
$ make install
This destination is a subdirectory of your home directory.
Once it is built and installed, you can copy the binary to /usr/local/bin or somewhere in your shell's PATH that makes sense to you. For me, my ${MACHTYPE} is x86_64 and I like having binaries in /usr/local/bin:
$ sudo cp ~areynolds/bin/x86_64/blat /usr/local/bin/blat
Adjust this to the particulars of your setup.
Downloading genomes
Once you have installed blat, the next step is to download a FASTA file for your genome of interest. If you wanted hg38, for instance:
$ for chr in `seq 1 22` X Y; do echo $chr; wget -qO- http://hgdownload.cse.ucsc.edu/goldenpath/hg38/chromosomes/chr$chr.fa.gz | gunzip -c - >> hg38.fa; done
Optimizing queries
Once you have this file hg38.fa, you can start doing queries, but it can help speed up searches if you first make an OOC file:
$ blat /path/to/hg38.fa /dev/null /dev/null -makeOoc=/path/to/hg38.fa.11.ooc -repMatch=1024
When you do searches, you'd pass this OOC file as an option to skip over regions with over-represented sequences.
Querying
Once you have this OOC file made, you can do searches with your FASTA file containing sequences of interest:
$ blat /path/to/hg38.fa /path/to/your-sequences.fa -ooc=/path/to/hg38.fa.11.ooc search-results.psl
The blat binary will write any search results to a PSL-formatted text file called search-results.psl. You can name this whatever you want.
The PSL format is described on the UCSC site.
Parallelization
If you have very many sequences, you can parallelize this by simply splitting up your input sequences file into smaller pieces, and running multiple blat processes, one process for each piece of your original sequences file, writing many PSL files as output.
Set operations
It can help to use a tool like BEDOPS psl2bed to convert PSL to a BED file to do set operations, but that depends on what you want to do with the results. In any case, to convert a PSL file to a sorted BED file:
$ psl2bed < search-results.psl > search-results.bed
Although this isn't exactly what I was asking about, we're having to rework our approach anyway, and BLAT will be very useful to that end. Thanks for the guide.