Dear all,
I have some splice junctions (in GFF3) that I ultimately want to convert to bam. I was thinking to convert first to bed myself and then to bam using bedToBam.
To test the second step I grabbed a bed-example from teh UCSC browser (each line encodes TWO exons) and ran a little test on it, converting to bam and then back to bed. This results in information loss:
nuvol:cufflinks htilgner$ cat test.bed
chr22 1000 5000 cloneA 960 + 1000 5000 0 2 567,488, 0,3512
chr22 2000 6000 cloneB 900 - 2000 6000 0 2 433,399, 0,3601
nuvol:cufflinks htilgner$ bedToBam -i test.bed -g hg19.genome.file > test.bam
nuvol:cufflinks htilgner$ bamToBed -i test.bam
chr22 1000 5000 cloneA 255 +
chr22 2000 6000 cloneB 255 -
Do you know why ? More importantly, is there an appropriate way to encode a spliced read in bam format ? How would that work ? Alternatively, is there a way to convert gff3 to bam directly ?
Thanks
I have some splice junctions (in GFF3) that I ultimately want to convert to bam. I was thinking to convert first to bed myself and then to bam using bedToBam.
To test the second step I grabbed a bed-example from teh UCSC browser (each line encodes TWO exons) and ran a little test on it, converting to bam and then back to bed. This results in information loss:
nuvol:cufflinks htilgner$ cat test.bed
chr22 1000 5000 cloneA 960 + 1000 5000 0 2 567,488, 0,3512
chr22 2000 6000 cloneB 900 - 2000 6000 0 2 433,399, 0,3601
nuvol:cufflinks htilgner$ bedToBam -i test.bed -g hg19.genome.file > test.bam
nuvol:cufflinks htilgner$ bamToBed -i test.bam
chr22 1000 5000 cloneA 255 +
chr22 2000 6000 cloneB 255 -
Do you know why ? More importantly, is there an appropriate way to encode a spliced read in bam format ? How would that work ? Alternatively, is there a way to convert gff3 to bam directly ?
Thanks
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