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Old 01-11-2012, 05:20 AM   #1
jordi
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Default 454 statistics

Hi all!
3 years ago we did a 454 run over a transcriptome data and using the Newbler release 1.1.03.24 we got some statistics in order to know the mean number of assembled reads per contig, the number of contigs with only 2 reads and so on...as we thought that a read could be assigned only to a single contig.
Today, we've used the 2.6 release software and the number of reads we've got from 454Allcontigs.fna ("numreads=" column) is larger than the total number of assembled reads. That's because a read could be assigned to a multiple contigs, isn't it? (as the contigs are "exons") If true, how kind of statistics do you advise in order to compare both sets of data??
From newblerMetrics I got that 83.48% of reads were assembled but I want to get such a value from the assembled contigs file as I've seen something like:
>contig00030 length=1 numreads=48 gene=isogroup00001 status=ig_thresh
t
>contig00031 length=6 numreads=4495 gene=isogroup00001 status=ig_thresh
CACTTC
>contig00032 length=3 numreads=61 gene=isogroup00001 status=ig_thresh
GgA
>contig00033 length=3 numreads=345 gene=isogroup00001 status=ig_thresh
gtA
>contig00034 length=2 numreads=2030 gene=isogroup00001 status=ig_thresh
TA
>contig00035 length=1 numreads=1914 gene=isogroup00001 status=ig_thresh
A


I hope I was clear enough!
Thanks in advance.
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Old 01-11-2012, 08:16 AM   #2
westerman
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Parsing the 454ReadStatus.txt file may the best solution.
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Old 01-11-2012, 08:54 AM   #3
jordi
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Thank you westerman. You are right, that seems to be the right place to find out the solution, but what kind of reads it's going to be assembled?? I mean: in 454NewblerMetrics file you have assembled reads, partial reads, singletons, repeat reads, outliers and tooshort (they appear in the last software release I think). I've read the flxlex blog (http://contig.wordpress.com/2010/03/...rics-txt-file/) and it seems that Assembled plus Partial and Repeat should be the number of aligned repeats...
However, what does it mean the "numreads=" in the 454Allcontigs.fna file??
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Old 01-11-2012, 09:09 AM   #4
westerman
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Quote:
Originally Posted by jordi View Post
However, what does it mean the "numreads=" in the 454Allcontigs.fna file??
I am going to guess here because I am deep into looking at other problems at the moment (although it should be easy to find out with a bit of digging) that the 'numreads=' is the count of all reads that contribute to the contig, no matter if that read maps uniquely to that contig or not.
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Old 01-12-2012, 12:10 AM   #5
flxlex
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Quote:
Originally Posted by westerman View Post
I am going to guess here because I am deep into looking at other problems at the moment (although it should be easy to find out with a bit of digging) that the 'numreads=' is the count of all reads that contribute to the contig, no matter if that read maps uniquely to that contig or not.
As far as I know, this is correct.
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