writing script to convert bam to bed

[camelbbs]

Hi,
I want to ask if anyone write a script to convert bam to bed.

I tried bamtools bamtobed but while i import the result bed files to IGV, i see it is very different to the bam files.

So I want to ask if anyone know this.

Thanks!!

[ETHANol]

See bedtools. Is your data RNA-seq data? If so you have to bed12 format to accommodate for gaps.

[camelbbs]

See bedtools. Is your data RNA-seq data? If so you have to bed12 format to accommodate for gaps.

Thanks, and how to view bed12 files in IGV?

[GenoMax]

If you only want to view BAM files is there is reason you are converting them to bed12?

Thanks, and how to view bed12 files in IGV?

[camelbbs]

If you only want to view BAM files is there is reason you are converting them to bed12?

Thanks. I just curious while I view bed and bam files in IGV, they show difference. bed file have coverage in intron region, but not in bam.

[camelbbs]

See bedtools. Is your data RNA-seq data? If so you have to bed12 format to accommodate for gaps.

I think bed12 file show the right thing. thanks. Can you explain what is the change in bed12 file comparing to bed.

bed file:

chr1    14396   14517   DJG84KN1:219:D0R66ACXX:7:1213:7112:52613/2      1       +
chr1    14407   14528   DJG84KN1:219:D0R66ACXX:7:1303:12836:72771/2     1       +
chr1    14407   14528   DJG84KN1:219:D0R66ACXX:7:1110:13035:15193/2     1       -
chr1    14407   14528   DJG84KN1:219:D0R66ACXX:7:1213:3980:31932/2      1       -
chr1    14411   14532   DJG84KN1:219:D0R66ACXX:7:1102:19850:62093/2     1       +
chr1    14421   14542   DJG84KN1:219:D0R66ACXX:7:1308:18446:95141/2     1       +
chr1    14452   14553   DJG84KN1:219:D0R66ACXX:7:1303:12836:72771/1     1       -
chr1    14453   14554   DJG84KN1:219:D0R66ACXX:7:1213:7112:52613/1      1       -
chr1    14460   14561   DJG84KN1:219:D0R66ACXX:7:1102:19850:62093/1     1       -
chr1    14472   14593   DJG84KN1:219:D0R66ACXX:7:1202:6747:36105/2      3       +

bed12 file:

chr1    14396   14517   DJG84KN1:219:D0R66ACXX:7:1213:7112:52613/2      1       +       14396   14517   255,0,0 1       121     0
chr1    14407   14528   DJG84KN1:219:D0R66ACXX:7:1303:12836:72771/2     1       +       14407   14528   255,0,0 1       121     0
chr1    14407   14528   DJG84KN1:219:D0R66ACXX:7:1110:13035:15193/2     1       -       14407   14528   255,0,0 1       121     0
chr1    14407   14528   DJG84KN1:219:D0R66ACXX:7:1213:3980:31932/2      1       -       14407   14528   255,0,0 1       121     0
chr1    14411   14532   DJG84KN1:219:D0R66ACXX:7:1102:19850:62093/2     1       +       14411   14532   255,0,0 1       121     0
chr1    14421   14542   DJG84KN1:219:D0R66ACXX:7:1308:18446:95141/2     1       +       14421   14542   255,0,0 1       121     0
chr1    14452   14553   DJG84KN1:219:D0R66ACXX:7:1303:12836:72771/1     1       -       14452   14553   255,0,0 1       101     0
chr1    14453   14554   DJG84KN1:219:D0R66ACXX:7:1213:7112:52613/1      1       -       14453   14554   255,0,0 1       101     0
chr1    14460   14561   DJG84KN1:219:D0R66ACXX:7:1102:19850:62093/1     1       -       14460   14561   255,0,0 1       101     0
chr1    14472   14593   DJG84KN1:219:D0R66ACXX:7:1202:6747:36105/2      3       +       14472   14593   255,0,0 1       121     0