TASSEL 5.0 GBSv2 pipeline using bam files as input and key file question

[Tevfik Hamdi Kitapci]

Hi,

I have 2 questions

1) I already aligned my fastq files to the reference genome. Can I use this aligned bam files as input for the TASSEL 5.0 pipeline instead of the fastq files

2) I have same sample sequenced on 2 different flow cells and sometimes on multiple lanes. If I put this information in the key files will those samples get merged ?

Example:

Flowcell
		
Lane
		
Barcode
		
DNASample
		
LibraryPlate
		
Row
		
Col
		
LibraryPrepID
		
LibraryPlateID
		
Enzyme
		
BarcodeWell
		
DNA_Plate
		
SampleDNA_Well
		
FullSampleName
	
	

		
Flowcell 1
		
5
		
CTCC
		
B73
		
IBM94_lowvol_Ape
		
A
		
1
		
250020986
		
450013677
		
ApoI
		
A01
		
IBM94
		
A01
		
B73:250020986
	
	

		
Flowcell 1
		
5
		
TTCTC
		
B73
		
IBM94_lowvol_Ape
		
B
		
1
		
250020994
		
450013677
		
ApoI
		
B01
		
IBM94
		
B01
		
B73:250020986
	
	

		
Flowcell 2
		
5
		
GCTTA
		
B73
		
IBM94_lowvol_Ape
		
C
		
1
		
250021031
		
450013677
		
ApoI
		
C01
		
IBM65
		
C01
		
B73:250020986
	

In this example I have 3 samples (they have the exact same DNASample and FullSampleName) but they are from different lanes of the same flow cell or from different flowcells. Will TASSEL pipeline merge these samples for the SNP calling ?

Thanks a lot
Best Regards
T. Hamdi Kitapci

[Tevfik Hamdi Kitapci]

I figured out the answer to my second question

https://bitbucket.org/tasseladmin/tassel-5-source/wiki/Tassel5GBSv2Pipeline/KeyFileExample

Sama sample names are merged 

One more question what if some of the wells on the plate is empty. Do I need to put a line for these empty wells in the key file or should I not include them ? If I need to include them is there a special sample name like "blank" or "empty" for these ?

Thanks

Hamdi

[Jeff Glaubitz]

Hi Hamdi,

You don’t need to include the empty wells in the key file, and yes, samples with the same name will be merged.

You can’t use your aligned bam files, as they are for each individual read.  The GBSv2 (or v1) pipeline needs alignments for each unique GBS tag.  A GBS tag represents a set of reads with the same 64 base (default) tag sequence.

Best,

Jeff

--
You received this message because you are subscribed to the Google Groups "TASSEL - Trait Analysis by Association, Evolution and Linkage" group.
To unsubscribe from this group and stop receiving emails from it, send an email to tassel+un...@googlegroups.com.
To post to this group, send email to tas...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/13419b50-80c0-4226-a012-6769c8e6eaac%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Tevfik Hamdi Kitapci]

Hi,

Thanks a lot for your reply. Is the same true for TASSEL 3.0 pipeline ? I am running in parallel both 3.0 and 5.0. 3.0 is completed and my samples are not merged. If I give the same sample name in the key file is that enough to merge the samples or do I need to do add another field in the key file to tell TASSEL to merge the same name samples ?

Thanks

Best Regards

Hamdi

[Jeff Glaubitz]

Hi Hamdi,

No, the same is not true for the Tassel3 pipeline, at least not automatically in the way that Tassel5-GBSv2 does.  In Tassel3-GBS you can use the -x option of the MergeTagsByTaxaFilesPlugin to merge samples with the same short name, as described in the documentation (pages 17-18), here:

https://bytebucket.org/tasseladmin/tassel-5-source/wiki/docs/TasselPipelineGBS.pdf

Best,

Jeff 

To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/f5b982c8-23b1-4a6d-bd76-156d2b69110b%40googlegroups.com.

[Nicholi Pitra]

can you opt to "not merge the names?" in tassel 5? 

[Nicholi Pitra]

look like the answer to my Q is no.