Our own data alignment and analysis: Difference between revisions
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>Shicheng |
>Shicheng |
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Line 20: | Line 20: | ||
=== fastq merge by indx === | === fastq merge by indx === | ||
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"; | |||
} | |||
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 01:11, 15 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
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"; }
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