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
Error when using filterBam on gsnap bam files
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Re: Error when using filterBam on gsnap bam files
Could this actually be the result of my READ not having an /1,/2 at the end of the header?
Re: Error when using filterBam on gsnap bam files
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
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