Our own data alignment and analysis: Difference between revisions
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>Shicheng |
>Shicheng |
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=== bismark alignment === | === bismark alignment === | ||
scp shg047@genome-miner.ucsd.edu:/media/Home_Raid1/zhl002/NAS2/LTS33T/mouse_WGBS/BAMfiles/* /home/shg047/oasis/mouse/alice/bam | |||
=== RD>10 Regions === | === RD>10 Regions === |
Revision as of 03:11, 16 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
- Trim fastq separately
my @file=glob("*gz"); my %file; foreach my $file(@file){ my @line=split/\.|_/,$file; push @{$file{$line[1].$line[3]}},$file; } foreach my $id(sort keys %file){ foreach my $sam(@{$file{$id}}){ print "$sam\t"; } print "\n"; } perl compile.pl > FastMatch.txt perl ~/bin/trimGolrePBS.pl FastMatch.txt submit
- bismark alignment separately
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
Trim_galore
bismark alignment
scp shg047@genome-miner.ucsd.edu:/media/Home_Raid1/zhl002/NAS2/LTS33T/mouse_WGBS/BAMfiles/* /home/shg047/oasis/mouse/alice/bam