Error when using filterBam on gsnap bam files
Posted: Mon Jun 27, 2016 3:20 pm
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
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