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-   -   Any suggestion on how to get to know the seq data is from which platform? (http://seqanswers.com/forums/showthread.php?t=47804)

arkilis 10-27-2014 03:13 PM

Any suggestion on how to get to know the seq data is from which platform?
 
Got some data from other lab people. They are not sure what platform it is. So I used the fastqc which can have a check on the read length and some tips on what platform it is. i.e. Quality scores across all bases (Sanger/ illumina 1.9 encoding). I would reckon it is probably from sanger.

Any other thoughts?

Thanks,

Brian Bushnell 10-27-2014 03:50 PM

Posting read headers may help; someone may recognized them. Also, a read length histogram (or range) might help narrow it down.

arkilis 10-27-2014 05:25 PM

Quote:

Originally Posted by Brian Bushnell (Post 153109)
Posting read headers may help; someone may recognized them. Also, a read length histogram (or range) might help narrow it down.

Thanks for answering.

One example line here is :

@M00474:102:000000000-A9000:1:1101:19225:1361 1:N:0:1
TGCTCACCTCGCCGCTGCACTGTGAAGCTCTCACCAACCCCGTAGTTGTTTCTGCACACGGTGTCCACCTGGCCCCGCCTGTCCTCCAGGATGTCCTTCTGGCTGTTCCAGGACTCGGCGACAGGCCGCCCTAGCTCCGTCACCGCCCGGTACTCCCCCCCGTCGCTGTCGAAGCGCACGAACTCCTCCTGGTTATAGAAGAGTCTTTCCAGGAACTGCACCCGCTCCGTCCCGTTGAAGAAATGACACTT
+
CACCCGGGGGBFGCGGGGFGGFGGDEGGFGGGGGGECFGGGGGDCFGFF,CFGGGGGGGD@FCGGGFGGGC,EFGGGGGG@FGGGGGFFFFGGFGGGGGG9<FGCFGGGGGFGFGGECFFDFB:BFGEFGGGDCFFGG@EGGGGGGGGG7E@EFGFGGG*CEEG:CEEGGGF5EDDGDEEGDGGGFFFGGFCFFFFF6D*)9CFGFFGFGG9:?(8?FF7?FB>>9>BB??FFFBFF()6<2:AABA7?B9

Any idea? Thanks again!

Brian Bushnell 10-27-2014 06:12 PM

Given that it's 251bp long, and the name look like the MiSeq convention, I would say that it's an Illumina MiSeq read.

arkilis 10-27-2014 06:39 PM

Quote:

Originally Posted by Brian Bushnell (Post 153119)
Given that it's 251bp long, and the name look like the MiSeq convention, I would say that it's an Illumina MiSeq read.

You are right. Mr. Genius! Just get confirmed with client. MiSeq.


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