Our own data alignment and analysis: Difference between revisions
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=== Transfer data from Genome-miner to TSCC=== | |||
* md5 to check the integrity | |||
cd /home/shg047/oasis/mouse/alice/raw | |||
for i in `ls *txt.gz` | |||
do | |||
md5sum $i > $i.md5 & | |||
done | |||
scp shg047@genome-miner.ucsd.edu:/media/NAS3_volume1/SeqStore2016/130104_SN1001/* ./ | |||
for i in `ls *txt.gz` | |||
do | |||
md5sum $i > $i.md5 & | |||
done | |||
=== fastq merge by indx === | === fastq merge by indx === | ||
for i in {01,02,04,05,06,07,09,10,11,12} | for i in {01,02,04,05,06,07,09,10,11,12} | ||
do | do |
Revision as of 23:25, 14 September 2016
Transfer data from Genome-miner to TSCC
- md5 to check the integrity
cd /home/shg047/oasis/mouse/alice/raw
for i in `ls *txt.gz` do md5sum $i > $i.md5 & done
scp shg047@genome-miner.ucsd.edu:/media/NAS3_volume1/SeqStore2016/130104_SN1001/* ./
for i in `ls *txt.gz` do md5sum $i > $i.md5 & done
fastq merge by indx
for i in {01,02,04,05,06,07,09,10,11,12} do cat s_*_1_Indx$i.txt.gz > Indx$i.read1.fq.gz & cat s_*_2_Indx$i.txt.gz > Indx$i.read2.fq.gz & done