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04-18-2011, 03:30 AM
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#1 |
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Member
Location: Sophia-Antipolis Join Date: Jun 2009
Posts: 10
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Bowtie alignment report
hello,
If someone can help me to understand bowtie (bowtie-0.12.7): I have a pseudo-miRNA sequence with adaptor: T01320202002122200123302010303131123 miRNAs - the base junction - adaptor bowtie -t -C -f -S -k 10 --best --strata --col-keepends /share/reference/bowtie_index/hg19_c -c T013202020021222001 bowtie -t -C -f -S -k 10 --best --strata --col-keepends /share/reference/bowtie_index/hg19_c -c 13202020021222001 are exactly the same so i can understand and give me a good results : chr4 143319992 18M CATCCTTCCCTGAGAAAC CM:i:0 chr19 54240159 18M TGCTTCCTTTCAGAGGGT CM:i:0 chr19 54264447 18M TGCTTCCTTTCAGAGGGT CM:i:0 chr19 54260055 18M TGCTTCCTTTCAGAGGGT CM:i:0 chr19 54228751 18M TGCTTCCTTTCAGAGGGT CM:i:0 Now: bowtie -t -C -f -S -k 10 --best --strata /share/reference/bowtie_index/hg19_c -c 0132020200212220012 chr1 77836010 18M CAAAGCTGAAAGGAAGCA CM:i:1 chr3 7953493 18M GTTTCTCAGGGAACCTAC CM:i:1 chrX 40255290 18M CAGAAGGAAAGTCTCCCA CM:i:1 chr17 14643968 18M CATAAGGAAAGTCTCCCA CM:i:1 chr14 22781068 18M ACGAAGGAAAGTTCTTTG CM:i:1 chr7 42334833 8M CATCCTTCCCTTCTCCCA CM:i:1 If someone can explain me how it is possible ? thanks |
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05-04-2011, 01:54 AM
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#2 |
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Member
Location: Sophia-Antipolis Join Date: Jun 2009
Posts: 10
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Is there someone who can answer to this question ?
thanks. |
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