04-14-2015

Done:

1, Install Alien Trimmer:

#Download and extract AlienTrimer_0.4.0.tar.gz;

#make the executable file:

a, install Java JDK using yum command, see the introduction here: http://www.cyberciti.biz/faq/centos-linux-6-install-java-sdk/

b, install AlienTrimer_0.4.0 according to the document in the doc fold.

2, Expand the disk space, as the original space is 19 GB, which is too small for actual use:

#add new virtual disk through setting in Virtual Machine;

#check out the new disk on centos:

$df -h

#operate in the root;

#/dev/sdb is the new disk location

$fdisk /dev/sdb

$n #set up new sector

$p #set up as primary sector

?$3 #choose among 1-4

$enter #choose beginning of the new sector

$enter #choose the end of the new sector

$t #format the sector

$8e #set up the LVM format

$w #write into the sector table

#restart the computer(centos6)

#add the sector into volumn group

$pvcreate /dev/sdb3

#display the bolumn group and remember the name Vg_centos63

$vgdispaly

#add the sdb3 to Vg_centos63

$vgextend Vg_centos63 /dev/sdb3

#extend the logic volumn in Vg_centos63 into 50 G

$lvextend -L 50G /dev/Vg_centos63-lv00

#resize the logic volumn

$resize2fs /dev/Vg_centos63-lv00

3, redownload all sRNA .fastq files to local directroy

4, Try to trim the adaptor end of the sequences, according to the manual.

Plan:

1, trim the adaptor end of all sequences

2, remap with bowtie2, on iplant

3, re-quantification with BedTools coverage, on iplant