Removing Duplicate Reads from Torrent data

vpp605 · 06-10-2013, 07:25 AM

Does anyone have any experience with removing duplicate reads from Ion Torrent data? Any idea if the 454-designed programs work well with Torrent (e.g., cd-hit-454)? Or any suggestions for other programs to use? The basis for this question is PCR-derived duplicates which I am anticipating will skew our analysis, and I would therefore like to remove them.

I should also mention that we do not have a reference genome to align reads to, as we are working with WGS metagenomic data.

jtackney · 07-05-2013, 01:23 PM

Hi - did you ever figure this out?

I've been using samtools "rmdup -s" but I don't think it's working as advertised for single-end reads of variable length....

eulbra · 09-12-2013, 07:09 PM

picard tools can do the job

IonTorrent · 09-13-2013, 07:26 AM

Hi there,

There is functionality within the Torrent Suite software for duplicate read marking, which can be enabled as desired. There is more information available via the Help tool within Torrent Browser or via Ion Community and the Torrent Suite documentation. There is also a FilterDuplicates plugin available as part of Torrent Suite.

I would also recommend follow up with your local Field Bioinformatics Scientist if you have any questions on these topics.

Quote:

Originally Posted by vpp605

Does anyone have any experience with removing duplicate reads from Ion Torrent data? Any idea if the 454-designed programs work well with Torrent (e.g., cd-hit-454)? Or any suggestions for other programs to use? The basis for this question is PCR-derived duplicates which I am anticipating will skew our analysis, and I would therefore like to remove them.

I should also mention that we do not have a reference genome to align reads to, as we are working with WGS metagenomic data.

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06-10-2013, 07:25 AM	#1
vpp605 Junior Member Location: Saskatchewan Join Date: Feb 2009 Posts: 6	Removing Duplicate Reads from Torrent data Does anyone have any experience with removing duplicate reads from Ion Torrent data? Any idea if the 454-designed programs work well with Torrent (e.g., cd-hit-454)? Or any suggestions for other programs to use? The basis for this question is PCR-derived duplicates which I am anticipating will skew our analysis, and I would therefore like to remove them. I should also mention that we do not have a reference genome to align reads to, as we are working with WGS metagenomic data. Last edited by vpp605; 06-10-2013 at 07:52 AM.

07-05-2013, 01:23 PM	#2
jtackney Member Location: Utah Join Date: May 2012 Posts: 16	Hi - did you ever figure this out? I've been using samtools "rmdup -s" but I don't think it's working as advertised for single-end reads of variable length....

09-12-2013, 07:09 PM	#3
eulbra Junior Member Location: Beijing Join Date: Mar 2012 Posts: 8	picard tools can do the job