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-   -   writing script to convert bam to bed (http://seqanswers.com/forums/showthread.php?t=23337)

camelbbs 09-13-2012 08:18 PM

writing script to convert bam to bed
 
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!!
http://postimage.org/image/68ynlxui3/

ETHANol 09-13-2012 10:11 PM

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

camelbbs 09-15-2012 10:16 AM

Quote:

Originally Posted by ETHANol (Post 83992)
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 09-17-2012 05:18 AM

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

Quote:

Originally Posted by camelbbs (Post 84117)
Thanks, and how to view bed12 files in IGV?


camelbbs 09-17-2012 11:25 AM

Quote:

Originally Posted by GenoMax (Post 84161)
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 09-17-2012 11:31 AM

Quote:

Originally Posted by ETHANol (Post 83992)
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:
Code:

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:
Code:

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



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