viewing read map data from Subread/Rsubread

akh22 · 04-21-2014, 07:17 AM

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.

shi · 04-27-2014, 04:55 PM

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.

Brian Bushnell · 04-27-2014, 06:25 PM

Quote:

Originally Posted by shi

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.

akh22 · 04-29-2014, 04:16 PM

I did sort and index BAM files but still IGB viewer can't open it.

Brian Bushnell · 04-29-2014, 04:23 PM

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.

GenoMax · 04-29-2014, 04:28 PM

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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04-21-2014, 07:17 AM	#1
akh22 Junior Member Location: Pittsburgh Join Date: May 2013 Posts: 7	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.

04-27-2014, 04:55 PM	#2
shi Wei Shi Location: Australia Join Date: Feb 2010 Posts: 235	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.

04-29-2014, 04:16 PM	#4
akh22 Junior Member Location: Pittsburgh Join Date: May 2013 Posts: 7	I did sort and index BAM files but still IGB viewer can't open it.

04-29-2014, 04:23 PM	#5
Brian Bushnell Super Moderator Location: Walnut Creek, CA Join Date: Jan 2014 Posts: 2,707	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.

04-29-2014, 04:28 PM	#6
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,143	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).