Blat search

[honey]

I was wondering is there an online tool or windows version of BLAT which can be used to align sequencing reads. The purpose is to find the mutations/ gaps. I dont know Unix.
Thanks

[Richard Finney]

http://genome.ucsc.edu/cgi-bin/hgBlat?command=start

[honey]

alignment of Hiseq reads

Thanks Richard,

Will it allow me to align the seqreads in FastQ format? I am sorry I forgot to mention this.

[Richard Finney]

No, blat uses fasta, not fastq.

See here for various solutions :http://stackoverflow.com/questions/1...a-with-sed-awk

You'll find that the online version is not very useful except for spot checking becasuse it limits the amount of data you can submit.

You'll want to get comfortable with the Unix/Linux command line if you're serious about nextgen. This inlcudes the standard tools "sed" , "awk', "grep", "sort" , "vi", etc. Knowing some programming (C, java, python or perl) will help.

If you're looking to align lots of data; blat may be a bit underpowered. Check out BWA and samtools for a more apporpriate tools for alignment and snp calling.

There's a serious learning curve involved iin all of those tools and the only way is keeping trying until you get it.

[honey]

Got It

I agrre...

Thanks