Hi,
I am using GSNAP and I have assigned the strand to my reads. I have tried to format my bam file in same way tophat's accepted_hits.bam file is formatted (I have placed an example of this below). However, when I run my sorted bam file through cufflinks, I get the following lines:
"BAM record error: found spliced alignment without XS attribute"
Does anyone have any idea as to what I could be doing wrong with my formatting? Thanks.
*Altered GSNAP file: output.bam*
*TOPHAT File: accepted_hits.sam*
I am using GSNAP and I have assigned the strand to my reads. I have tried to format my bam file in same way tophat's accepted_hits.bam file is formatted (I have placed an example of this below). However, when I run my sorted bam file through cufflinks, I get the following lines:
"BAM record error: found spliced alignment without XS attribute"
Does anyone have any idea as to what I could be doing wrong with my formatting? Thanks.
*Altered GSNAP file: output.bam*
HTML Code:
D8FF8JN1:127:C066VACXX:8:1207:12974:19520 147 chr1 4610 40 83M140N16M = 4311 0 CGGCAGAGGAGGGATGGAGTCTGACACGCGGGCAAAGGCTCCTCCGGGCCCCTCACCAGCCCCAGGTCCTTTCCCAGAGATGCCCTTGTGCCTCATGAC DDCADDC@CCDA>CC@@@DDDCADDDDDDDDCDCCCB?DCDDCFFHHBHHDGC=CJIIJGHCHEIIGEHE3JJJJIIHFEGCJIIIIFHHGHDDFDD?C NM:i:1 XS:A:- NH:i:1 D8FF8JN1:127:C066VACXX:7:1103:12412:135532 163 chr1 15 40 75M = 41 101 ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC 144=BDHHHHHJJJJJJJJJJJJJJJJJIJJJJJJGIJJFHJJJJJJJIJIJJIJIGIHHHHFFFFFEEDEDCDB NM:i:0 XS:A:- NH:i:1 D8FF8JN1:127:C066VACXX:7:1103:12412:135532 83 chr1 41 40 69M6S = 15 -101 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCACTCCAC DABBCDEEDBDFFFFHAHHJIGDJIIHFFJJJIHFJJHHGBJJIHHDJJIGHHJJIHHGJJJIHHHHFCFEFFFC NM:i:0 XS:A:- NH:i:1
HTML Code:
D8FF8JN1:127:C066VACXX:8:2206:17700:177847 113 chr1 5783 1 28M659N71M = 5783 0 TCGACCACTTCCCTGGCAGCTCCCTGGACTGAAGGAGACGTGCTGCTGCTGCTGTCGTCCTGCCTGGCGCCTTGGCCTACAGGGGCCGCGGTTGAGGTT DDDCDDCDDDBBCC<3(BDDBDDDDDDEDDDDDDDDDDDDDDDDDDDDDDDDDDDDFFFHHHHJJJJJJJJIIJIJJIJJJJJJJJJHHHHHFFDB=+@ NM:i:4 XS:A:- NH:i:3 CC:Z:chrX CP:i:154906249 D8FF8JN1:127:C066VACXX:8:1307:2101:94989 129 chr1 6590 0 39M88N60M = 6590 0 GGGGCGGTGGGGGTGGTGTTAGTACCCCATCTTGTAGGTCTGCCTTGAGAGGCTCGGCTACCTCAGTGTGGAAGGTGGGCAGTTCTGGAATGGTGCCAG CCFFFFFHHHHGJ@BD<DDDCECEEDDDDDDDDDDDDDCCDDDDDDDDDDDDCDDDDBB@CDDCCC@@>@B(4>?9:?B?CB?>@DCDAA@AC+4:A@C NM:i:1 XS:A:- NH:i:7 CC:Z:chr15 CP:i:100331773 D8FF8JN1:127:C066VACXX:8:1307:2101:94989 65 chr1 6590 0 39M88N60M = 6590 0 GGGGCGGTGGGGGTGGTGTTAGTACCCCATCTTGTAGGTCTGCCTTGAGAGGCTCGGCTACCTCAGTGTGGAAGGTGGGCAGTTCTGGAATGGTGCCAG CCFFFFFHHHHGJ@BD<DDDCECEEDDDDDDDDDDDDDCCDDDDDDDDDDDDCDDDDBB@CDDCCC@@>@B(4>?9:?B?CB?>@DCDAA@AC+4:A@C NM:i:1 XS:A:- NH:i:7
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