Error when using filterBam on gsnap bam files

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PhilSchiffer
Posts: 2
Joined: Mon Jun 27, 2016 3:14 pm

Error when using filterBam on gsnap bam files

Post by PhilSchiffer »

Hi!

I am following this protocol
http://bioinf.uni-greifswald.de/bioinf/ ... Aseq.GSNAP
and am getting a "wrong" output from this step
filterBam --uniq --paired --in rnaseq.ss.bam --out rnaseq.f.bam.
My version is augustus3.0.3

My input bam file looks like this:
SRR2681987.1 0 NODE_652_length_22097_cov_9.33573_ID_123088 3287 40 100M1S * 0 0 GTAGGGTCTGTACTGTTTTATGTACAACAGTTACAGCACTCAACATCAGCAGTTCATTGTTTGATAAATCAGATCTATCAAATACTCTGAACAGATGGCTA B@@DDDF?BC?CFB
SRR2681987.1 16 NODE_652_length_22097_cov_9.33573_ID_123088 3330 40 101M * 0 0 CATCAGCAGTTCATTGTTTGATAAATCAGATCTATCAAATACTCTGAACAGATGGCTCATTATCGTAGGTAGAAACTGAATAGCATGAGCTGAGAGCCTAG @CCCA;>@>;@@EE
SRR2681987.5 16 NODE_8628_length_2173_cov_9.20626_ID_327294 1431 40 50M * 0 0 GATTCATAGGGGAGTTCAGGGGGATGGCTAGGCGACGTTTTGTATCAAAT 7DCIHCB3FD?9*GBB1IGD?BB?1)*C<)AC<2+@C?HDA,,EDA+@?? MD:Z:5
SRR2681987.5 16 NODE_6009_length_3392_cov_18.5629_ID_265836 819 37 88M * 0 0 TCCAACTGTGTGAATACACCCGTGAAGAGTACGAACCCTCGCAGAAACTTTCTGATCACGACAAGGACAACATGTTGAACAAACTCAG AAAAA??AA>>>>

But the output only has the header

BAM^A<A3>t&^@@HD VN:1.0 SO:queryname
@SQ SN:NODE_10000_length_1788_cov_2.9422_ID_470146 LN:1788
@SQ SN:NODE_10001_length_1788_cov_13.0157_ID_472302 LN:1788
@SQ SN:NODE_10002_length_1787_cov_7.25301_ID_470193 LN:1787
@SQ SN:NODE_10003_length_1787_cov_3.98976_ID_470470 LN:1787
@SQ SN:NODE_10004_length_1786_cov_3.93309_ID_559464 LN:1786
@SQ SN:NODE_10005_length_1786_cov_1.94635_ID_470484 LN:1786
@SQ SN:NODE_10006_length_1786_cov_4.73659_ID_470498 LN:1786

It is also not being readable to samtools view, but to zless.

Any help with this would be highly appreciated.

Kind regards

Philipp
PhilSchiffer
Posts: 2
Joined: Mon Jun 27, 2016 3:14 pm

Re: Error when using filterBam on gsnap bam files

Post by PhilSchiffer »

Could this actually be the result of my READ not having an /1,/2 at the end of the header?
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katharina
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Joined: Wed Nov 18, 2015 6:14 pm
Location: Greifswald
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Re: Error when using filterBam on gsnap bam files

Post by katharina »

Hi Phil,

I am not sure. I would need access to a toy data set of your bam file.

It should not be a matter of /1 /2 read naming convention, anymore, since we fixed that issue a while ago.

I am apologize for the long silence, I had been on parental leave. If you are still interested, please contact me via e-mail and send a toy data set so that I can trace the error.

Katharina
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