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Old 10-20-2013, 07:02 PM   #7
pengchy
Senior Member
 
Location: China

Join Date: Feb 2009
Posts: 116
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Hi all,

this problem seems still unresolved.
GTF was recommended by Tophat2 paper if available.
In my case, only one line has the problem in one bam file:
Code:
        73      scaffold210     158009  50      30M26178N70M    *       0       0       GTACGAGTCGTTCTGCCGGCCGCCGTGCTCGGAGTCGCCGTTGACGATCCAGACGATGTGCGGCGCGGGCTTGGCGGAGCCGGAGCTGCAGTTGGCGTGC  $#$%&&&#%$"&"%("')&!&)''&!"%%(""!$!"!!"""#%%"$%%%%$"!"!!!!!"%!"%$"#%%%%""%%!!!!"$%"!!"%$$!!!!!!!!!!!  AS:i:-12        XM:i:2  XO:i:0  XG:i:0  MD:Z:78C18C2    NM:i:2  XS:A:-  NH:i:1
Where, the read name was not printed successfully.

I filtered this line by:
awk '$1!~/^[0-9]/'

Last edited by pengchy; 10-20-2013 at 07:06 PM. Reason: add awk command
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