User: caelyn5201314
caelyn5201314 • 10
- Reputation:
- 10
- Status:
- New User
- Location:
- China/Beijing/Chinese Academic Of Science
- Last seen:
- 3 years, 1 month ago
- Joined:
- 3 years, 11 months ago
- Email:
- c************@gmail.com
Posts by caelyn5201314
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... yes, this is my annotation file
Chr1 irgsp1_rep exon 2983 3268 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; gene_name "Os01g0100100"; oId "Os01t0100100-01"; tss_id "TSS1";
Chr1 irgsp1_rep exon 3354 3616 . + . gene_id ...
written 3.7 years ago by
caelyn5201314 • 10
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... The annotation file is correct...if i use -g then nothing wrong
...
written 3.7 years ago by
caelyn5201314 • 10
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... Hi,all!
I use the cufflinks with the parameter -G and found that all the FPKM values are 0.
this is my command
/share_bio/nas2/zhangz_group/xial/software/cufflinks-2.2.1.Linux_x86_64/cufflinks -o /share_bio/nas2/zhangz_group/xial/test/$Filename2[$i]/$realFiles[$j]/cufflinks_result -p 8 -G /shar ...
written 3.7 years ago by
caelyn5201314 • 10
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Comment:
C: Help in NGS QC Toolkit
... ok...thank you !!!:)
...
written 3.8 years ago by
caelyn5201314 • 10
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Comment:
C: Help in NGS QC Toolkit
... I print scalar(@Filename2) and print @filename ,it same !
...
written 3.8 years ago by
caelyn5201314 • 10
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Comment:
C: Help in NGS QC Toolkit
... @filename2 is the length of the array
...
written 3.8 years ago by
caelyn5201314 • 10
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Answer:
A: Help in NGS QC Toolkit
... thank you RamRS and Geek_y !!!!! It worked !!! thanks a lot !!!!
...
written 3.8 years ago by
caelyn5201314 • 10
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Comment:
C: Help in NGS QC Toolkit
... oh,i have a lot files, like :
DRP000568
SRP222222
SRP999999
and "next unless" is just want to test if one file works out
...
written 3.8 years ago by
caelyn5201314 • 10
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Comment:
C: Help in NGS QC Toolkit
...
#!/usr/bin/perl
use strict;
use warnings;
opendir(FILE,"/share_bio/nas2/zhangz_group/xial/test") or die "Can't open dir ";
my @Filename=readdir(FILE);
closedir(FILE);
my @Filename2 = grep(/^[A-Z]/,@Filename);
for (my $i=0;$i<@Filename2;$i++)
{
next unless ($Filename2[$i] eq "DRP000568"); ...
written 3.8 years ago by
caelyn5201314 • 10
• updated
3.8 years ago by
RamRS ♦ 18k
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Comment:
C: Help in NGS QC Toolkit
... system "perl /leofs/zhangz_group/xial/NGSQCToolkit_v2.3.3/QC/IlluQC.pl -pe /leofs/zhangz_group/xial/data-fastq/Pair-end/$Filename2[$i]/$file1 /leofs/zhangz_group/xial/data-fastq/Pair-end/$Filename2[$i]/$file2 N A –t 2 –l 70 –s 20";
...
written 3.8 years ago by
caelyn5201314 • 10
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