runData/file/numberOfReads in 454NewblerMetrics.txt ?

[dan]

I don't understand why I get two values for 'numberOfReads' and 'numberOfBases' in the runData/file section of 454NewblerMetrics.txt:

/***************************************************************************
**
**      454 Life Sciences Corporation
**         Newbler Metrics Results
**
**      Date of Assembly: 2012/09/18 13:55:53
**      Project Directory: /home/training/pp-assembly-workshp-bk-noPE
**      Software Release: 2.6 (20110517_1502)
**
***************************************************************************/

/*
**  Input information.
*/

runData
{
	file
	{
		path = "/home/training/Data/Newbler/BAC_Pool_3_SKS_SK35_Reads_RL5.sff";

		numberOfReads = 281603, 237939;
		numberOfBases = 110946882, 93033055;
	}

}

/*
**  Operation metrics.
*/

runMetrics
{
	inputFileNumReads  = 281603; 
	inputFileNumBases  = 110946882; 

	totalNumberOfReads = 237939; 
	totalNumberOfBases = 93033055; 
...

I read the manual (around page 137 of Manual-v2.6_PartC_Assembly_and_Mapping_May2011.pdf), but it doesn't explain why multiple values would appear here.


Thanks for any help,
Dan.

[vivek_]

I think its <number of reads/bases>, <number of reads/bases after trimming>.

[dan]

Hmm... That's a good point, because I don't know where else the trimming / screening is reported.

Shame documentation is lacking.

[dan]

So what does equivalent set of numbers mean in the case of PE?

pairedReadData
{
	file
	{
		path = "/home/training/Data/Newbler/SK3911_PairedReadOne_HNFY28401.sff";

		numberOfReads = 469316, 656913;
		numberOfBases = 160822071, 126727498;
		numWithPairedRead = 234009;
	}

}

[vivek_]

I think its the same except each of the paired end reads is counted as a different trimmed read.

[dan]

I don't see how there could be 469k reads, 657k trimmed.

[vivek_]

I'm not totally sure but I think read_1 & read_2 of a pair are counted individually for num. of trimmed reads.

[dan]

Weird! heh.

[RCJK]

Check this out for much more info:

http://contig.wordpress.com/category/newbler-output/

[dan]

That's really nice, but I still don't see it described

[RCJK]

http://contig.wordpress.com/2010/03/11/newbler-output-i-the-454newblermetrics-txt-file/