AUGUSTUS Forum

Posted: **Mon Jun 20, 2016 8:15 pm**

Hi everyone,

I,m trying to annotate the genome of a newly assembled ant. I am following your tutorial here:http://bioinf.uni-greifswald.de/bioinf/ ... s.Augustus, and I'm trying to obtain hints for gene prediction in augustus. I'm having some problem in getting Exon-exon junction hints. After aligning read to the genome scaffolds (a test of 10M reads) I run filterBAM as described in the tutorial:

Code: Select all

filterBam --uniq --paired --in Aligned.out.bam --out Aligned.out.sf.bam

But I get this:

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processed line 300001
------------------------------------- 
Summary of filtered alignments: 
------------------------------------- 
unmapped        : 0
percent identity: 561
coverage        : 5372
not paired      : 358611
quantiles of unspliced insert lengths:
[Quantiles]:vector::_M_range_check; insertlen.size()=0
unique          : 0
------------------------------------- 
Cmd line: 
filterBam --uniq --paired --in Aligned.out.bam --out Aligned.out.sf.bam 
------------------------------------- 
Elapsed time: 0.000 seconds.

but the output file Aligned.out.sf.bam looks empty. Could it be that the bam file generate with STAR instead of Tophat is the reason why I got this error? Would you help me?

Thank you a lot
Francesco

Posted: **Fri Mar 31, 2017 8:38 am**

Hi Francicco,

I apologize for the long silence, I was on parental leave.

If you are still having this problem, please send me a toy data set via e-mail and I will look into this.

In general, I recommend you skip interative alignment. It is a procedure that we developed before today's RNA-Seq alignment tools worked the way they do, now. Tophat2 - for example - does a good job on intron junctions. I recommend you just use it and skip iterative alignment.

Best,

Katharina

AUGUSTUS Forum

filterBAM error

filterBAM error

Re: filterBAM error