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Thread | Thread Starter | Forum | Replies | Last Post |
casava 1.8 bam conversion to gatk bam | kingsalex | Bioinformatics | 1 | 02-14-2012 12:47 PM |
How do I convert 454 ace to a regular ace? | lskatz | Bioinformatics | 5 | 11-22-2010 08:31 AM |
TOPHAT EMPTY accepted_hits.bam ISSUE | waterboy | Bioinformatics | 1 | 11-16-2010 09:48 AM |
ACE to SAM/BAM pile-up | JueFish | Bioinformatics | 3 | 06-16-2010 09:39 AM |
Fasta to Ace conversion | Farhat | Bioinformatics | 19 | 05-15-2010 07:08 PM |
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#1 |
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Location: Purdue University, West Lafayette, Indiana Join Date: Aug 2008
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I have heard that the "next" version of the Roche 454 software will include a .bam output format.
Until then (and presuming this is actually the case) I am stuck with the brutal amos2bnk methodology outlined here: http://sourceforge.net/apps/mediawik...SAM_Conversion There are numerous non-documented gotchas ready to pounce on the misguided novice who attempts this protocol. But I have managed to traverse the procedure a couple of times and emerge bloodied but (largely) unbroken. One final issue involves actually view the resulting .bam file in IGV. (BTW, you definitely want to turn off "show soft-clipped bases" in the preferences.) I think the issue derives from the crazy long cigar strings produced. Some of this is to be expected because of the 454's well-known homopolymer issues. However, it looks to me like the cigar strings are being produced from the padded reads in the .ace file. That legions of "deletions" versus the consensus are shown in the viewer. Anyone seen this? Anyone have solution to suggest? -- Phillip |
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#2 |
Peter (Biopython etc)
Location: Dundee, Scotland, UK Join Date: Jul 2009
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Do you have to have a SAM/BAM file? Why not stick with the ACE file and use a viewer that supports that?
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#3 |
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Location: Purdue University, West Lafayette, Indiana Join Date: Aug 2008
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Here is an example cigar string produced:
Code:
69S10M1P4M1P2M1P12M1P11M1P2M1P10M1P18M1P2M1P3M1P30M1P6M1P3M1P1M1P3M1P9M1P9M1P5M1P7M1P1M1P1M2P7M1P1M1P2M1P2M2P3M1P6M1P3M1P3M1P6M1P3M1P5M1P3M1P1M3P1M3P1M1P1M1P1M4P1M1P1M2P4M1P1M1P2M1P3M1P1M1P5M1P2M1P7M1P2M1P7M2P5M1P1M1P2M1P1M1P2M1P3M1P2M1P1M1P1M1P1M2P1M1P3M1I1D9M1P1M1P1M1P3M2P1M1P1M1P3M1P1M1I1D6M1P2M1P3M1I2D2M1I2M1I1D2M1P7M1P12M2P6M1P2M1D1I15M1P9M1P3M1P4M1P1M1P3M1P3M1P22M1P7M1P26M1P15M1P1M1P4M1P6M2P9M1P6M1P2M2P2M1P9M1P2M1P3M4S -- Phillip |
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#4 | |
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Location: Purdue University, West Lafayette, Indiana Join Date: Aug 2008
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I really like IGV. The only ACE file viewer I use is consed. Great for BAC sized assemblies. Not good for full bacterial genomes. Do you have an ACE viewer you would recommend? -- Phillip |
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#5 |
Peter (Biopython etc)
Location: Dundee, Scotland, UK Join Date: Jul 2009
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I personally use Tablet for viewing ACE files (and SAM/BAM files too). It supports some other formats as well: http://bioinf.hutton.ac.uk/tablet/
If you are interested in editing the ACE file, GAP4 or GAP5 would be worth a look too. |
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#6 | |
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Location: Berlin, DE Join Date: May 2008
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#7 | |
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Location: Purdue University, West Lafayette, Indiana Join Date: Aug 2008
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It did not work for the BAM file I tried. I get: SAM validation error: ERROR: Record 44, Read name H-148_49:1:1208:17598:140372, Mate Alignment start should != 0 because reference name != *.But we are running samtools 0.1.5, so possibly that is the issue. Anyway, thanks for the advice. -- Phillip |
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#8 | |
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http://sourceforge.net/projects/samtools/ the current version of samtools is 0.1.6 *****Note added after posting: Arrgg! The most recent version of samtools is 0.1.16! I seem to be unable to read decimal numbers today. Well, I don't want to let the facts get in the way of my (lame) joke. So, please continue reading... ***** Possibly Tablet works so well because it was sent back in time by coders from the future using advanced methodologies? But they failed to account for the lack of certain key dependencies? Ah well, it works for ACE files... -- Phillip Last edited by pmiguel; 06-23-2011 at 06:06 AM. Reason: Erroneous info on current samtools version |
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#9 |
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We've got the same issue. As we only do resequencing the ACe file format is definitely not the best solutoin for outputting alignment (especially against the human reference genome, as it is realyy large even for small projects).
Tablet can visualize ACE files, however it is a pain to get some additional data to visualize easily (in our case gene annotations). I#M really looking forward to the next software version with BAM output. I was already thinking of coding something myself... Does anyone know when the new version will arrive? |
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#10 |
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Well, this is little more than speculation...
But, generally major chemistry/hardware releases are accompanied by a new software version. The new longer read chemistry upgrades are either happening now or rolling out over the summer. So that would suggest that the answer is "soon"? -- Phillip |
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#11 | |
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#12 | |
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Tablet tries to read the statistics (specifically read counts per contig) for a BAM's index file (.bai) and will warn if it can't do this, which usually happens if the index file was created using a version of samtools earlier than 0.1.8, which is the first version (we're aware of) that added these stats. It's been available since last summer. |
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#13 | ||
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Location: Purdue University, West Lafayette, Indiana Join Date: Aug 2008
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The Tablet guys responded to an email I sent them about this issue with: Quote:
-- Phillip |
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#14 |
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v2.6 is a part of the upgrade package for the XL+ upgrade. Last I've heard they (my local Roche reps) seem somewhat confident that the upgrade will launch at the end of June. A recent article on GenomeWeb also mentioned end of June, but we'll see. That's what they were saying last year.
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#15 | |
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