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Old 04-17-2013, 08:06 AM   #1
kanewong
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Default How to change MapSplice output(txt format) into bed format?

Hi all,

I have run several splice-junction tools such as tophat, splicemap. They give me bed file results which can be easily handled by bedtools. However, Mapsplice produces txt file format. Is there any method I can change it into bed file?

Actually Mapsplice produces txt file output because its output contains more information than normal splice-junction tools do. But currently I just need to use Bedtool to compare the overlap of the splice junctions(chr start to chr end). Therefore, besides the first several columns, the others are not needed.

Tophat, Splicemap format(bed):

chr1 3840 4068 JUNC00000001 25 + 3840 4068 255,0,0 2 73,73 0,155
chr1 4203 4557 JUNC00000002 42 + 4203 4557 255,0,0 2 73,72 0,282
chr1 4530 4780 JUNC00000003 44 + 4530 4780 255,0,0 2 75,75 0,175


Mapsplice format(txt):
chr1 3913 3996 JUNC_1 15 + 3913 3996 255,0,0 2 63,73, 0,157, 2.523211 5 GTAG 0.999585 1.000000 0 1 0.133333 15 0 0 0 0 0 0 15 2

chr1 4276 4486 JUNC_2 22 + 4276 4486 255,0,0 2 73,70, 0,281, 2.815205 5 GTAG 0.998950 1.000000 0 1 0.045455 22 0 0 0 0 0 0 22 2

chr1 4605 4706 JUNC_3 19 + 4605 4706 255,0,0 2 56,70, 0,172, 2.552085 5 GTAG 0.999495 1.000000 0 1 0.157895 19 0 0 0 0 0 0 19 4


Thank you
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Old 04-17-2013, 08:31 AM   #2
GenoMax
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Are you a bench biologist or a computer scientist?

From your other posts it sounds like the latter so it should be easy for you to select the columns you need from the Mapsplice output (once you understand what it contains) so you can do the analysis you need for your thesis.
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Old 04-17-2013, 07:15 PM   #3
kanewong
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Quote:
Originally Posted by GenoMax View Post
Are you a bench biologist or a computer scientist?

From your other posts it sounds like the latter so it should be easy for you to select the columns you need from the Mapsplice output (once you understand what it contains) so you can do the analysis you need for your thesis.
Hi GenoMax, yes I am now studying a master degree of bioinformatics, but before that, I studied biochem for all time. So I am a newbie to this field.
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Old 04-17-2013, 07:57 PM   #4
kanewong
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Someone suggests me to use cut command to transfer it to bed file, i will try
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