ubuntu shortcuts

find ~/mydir -iname '*.htm' -exec rm {} \;

50 useful unix codes

http://www.thegeekstuff.com/2010/11/50-linux-commands/

interpreting chromatogram: very useful post from uni michigan

http://seqcore.brcf.med.umich.edu/doc/dnaseq/interpret.html

try link

Try this blog. Love the posts. http://squamules.blogspot.com/2011/08/using-sequencher-for-multiple-sequence.html

use sequencher, its a good soft, but not free. demo version is good, but u cant save, export copy paste!

Understanding transcriptome assembly in newbler

what is the difference between isotig , isogropu and contigs??

• For a quick view Isogropus are made of isotigs and isotigs are made of contigs

• Normally one gene should have one transcript, but due to splice variation one gene can have many transcripts. suppose a gene is made of 3 exons, exon 1, exon2 and exon 3. It will generate 3 contigs in newbler, contig 1, contig 2 and contig 3. Due to splice variation the final transcript can be consist of exon1+exon2+exon3 or exon1+exon3 etc.. Thus we get 2 type of variation here, these two are called isotig 1 and isotig 2. isotig 1 consist of contig 1+ contig 2 + contig3 and isotig 2 consists of contig 1+ contig 3. These two isotigs are variation of one transcript. So these 2 isotigs combinedly fall in one isogroup.

• It means that isogroups are transcripts, isotigs are splice variants of one transcript and contigs are separate exons.

• Sometimes primary transcripts can have introns or UTR regions which are also got in form of contigs

• sometimes similar isotigs can be found if come from different sister chromosomes, it can be identified by clustering with cdhit.

odd number of sequences in paired end file

sed '$d' filename.txt

A very important blog

http://contig.wordpress.com/2010/04/13/newbler-output-iii-the-454contiggraph-txt-file/