samtoroc.sh -- no truePositive hits

Question

[mschmid]

I am in the process of compairing different short read mappers for a task.

I want to use BBMap's "randomreads.sh" & "samtoroc.sh" to do that. (Version 36.84)

With BWA it worked like a charm. But I get strange results when I use bbmap.sh to map my simulated reads.

Commands are the following:

randomreads.sh ref=../pe_meta_contigs_minLength.fasta paired=f mininsert=200 maxinsert=1000 length=300 coverage=200 spaceslash=f
bbmap.sh ref=../pe_meta_contigs_minLength.fasta in=reads_B1_3938618x300bp_0S_0I_0D_0U_0N.fq.gz out=SE_bbmap_onSimulatedData.sam
samtoroc.sh in=SE_bbmap_onSimulatedData.sam reads=3938618 > roc.txt

Result:

ROC Curve for SE_bbmap_onSimulatedData.sam
minScore    mapped  retained    truePositiveStrict  falsePositiveStrict truePositiveLoose   falsePositiveLoose  falseNegative   discarded   ambiguous
46  92.9880 92.9880 0.0000  92.9880 0.0000  92.9880 7.0120  0.0000  0.0000
45  96.6744 96.6744 0.0000  96.6744 0.0000  96.6744 3.3256  0.0000  0.0000
44  98.1959 98.1959 0.0000  98.1959 0.0000  98.1959 1.8041  0.0000  0.0000
43  99.1110 99.1110 0.0000  99.1110 0.0000  99.1110 0.8890  0.0000  0.0000
42  99.1839 99.1839 0.0000  99.1839 0.0000  99.1839 0.8161  0.0000  0.0000
41  99.1997 99.1997 0.0000  99.1997 0.0000  99.1997 0.8003  0.0000  0.0000
40  99.2043 99.2043 0.0000  99.2043 0.0000  99.2043 0.7957  0.0000  0.0000
39  99.2068 99.2068 0.0000  99.2068 0.0000  99.2068 0.7932  0.0000  0.0000
38  99.2070 99.2070 0.0000  99.2070 0.0000  99.2070 0.7930  0.0000  0.0000
37  99.2072 99.2072 0.0000  99.2072 0.0000  99.2072 0.7928  0.0000  0.0000
35  99.2072 99.2072 0.0000  99.2072 0.0000  99.2072 0.7928  0.0000  0.0000
32  99.2073 99.2073 0.0000  99.2073 0.0000  99.2073 0.7927  0.0000  0.0000
3   99.9650 99.2073 0.0000  99.2073 0.0000  99.2073 0.0350  0.0000  0.7578
0   99.9650 99.2073 0.0000  99.2073 0.0000  99.2073 0.0350  0.0000  0.7578

[Brian Bushnell]

That's odd! I'll look into it and get back to you...

Answer 1

[Brian Bushnell]

Sorry about that! The problem is the trailing " /1" on the read names. Bwa trims this off but BBMap doesn't by default. So you can either remove it by mapping with BBMap and adding the "trd" flag (which stands for "trim read description"), or using the "addslash=f" flag when generating the synth reads with RandomReads.

[mschmid]

Thanks Brian! What about adding this option to the randomreads.sh help? I think it is not mentioned, or did I miss it? Maybe you even mention that for samtoroc.sh it should be set to false?

[Brian Bushnell]

Oh, I fixed it so the problem won't happen any more once I upload the latest version. It was unintentional.