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Old 04-21-2014, 08:17 AM   #1
akh22
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Default viewing read map data from Subread/Rsubread

Hi all,

I've been trying to view mapping BAM outputs from Rsubread by using IGV and IGB but these viewers don't appear to like BAM files created by Rsubread. Can anybody recommend other map viewers or any pointers to to accomplish this ?

Thanks in advance.
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Old 04-27-2014, 05:55 PM   #2
shi
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Reads in BAM output from Subreads are in the same order as in your input FASTQ file. You need to sort them by chromosomal locations before feeding them to IGV or IGB.
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Old 04-27-2014, 07:25 PM   #3
Brian Bushnell
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Quote:
Originally Posted by shi View Post
Reads in BAM output from Subreads are in the same order as in your input FASTQ file. You need to sort them by chromosomal locations before feeding them to IGV or IGB.
More precisely, you need to sort (by coordinate, as stated) AND index them. You can do both with Samtools or Picard.
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Old 04-29-2014, 05:16 PM   #4
akh22
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I did sort and index BAM files but still IGB viewer can't open it.
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Old 04-29-2014, 05:23 PM   #5
Brian Bushnell
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I have never used IGB, just IGV.

Anyway...

It would help if you described the command lines you used, and posted the header of the bam file (if it's reasonably short), and the specific error messages you get.
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Old 04-29-2014, 05:28 PM   #6
GenoMax
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Are you getting a specific error or is nothing happening when you try to open the file?

I do not know about IGB but for IGV you may need to adjust the memory assigned to IGV at startup (or use the appropriate web launcher).
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