stampy output

[manore]

Hi,

I get the following information using stampy

stampy...
stampy: # Nucleotides (all/1/2): 408825780 204412890 204412890
stampy: # Variants: 5721043 2786247 2934796
stampy: # Fraction: 0.0140 0.0136 0.0144
stampy: # Paired-end insert size: 167.0 +/- 25.7 (1884265 pairs)
stampy: Done

Could anyone give me an explanation about the nucleotides, variants and fraction line ?

Thanks in advance

[Jon_Keats]

Nucleotides = Nucleotides aligned
- All = All reads
- 1 = Forward reads
- 2 = Reverse reads
Variants = Non-reference bases aligned (ie. SNPs and such)
- All three as before
Fraction = Fraction of variants discovered in the total number of bases aligned
Paired-end Insert size = The distance/size of DNA insert between the two adaptors
[For adaptor]-ForwardRead----->------------<------ReverseRead-[Rev adaptor]

[manore]

Thanks so much

[nr23]

I've just finished running Stampy for the first time. I've got the following output:


stampy: Mapping...
stampy: # Nucleotides (all/1/2): 9581823944 4790911972 4790911972
stampy: # Variants: 811646897 406424420 405222477
stampy: # Fraction: 0.0847 0.0848 0.0846
stampy: # Paired-end insert size: 141.5 +/- 42.7 (29776104 pairs)
stampy: Done

And an output file. What format is the output file in? I didn't specify while running stumpy - I assume it's SAM?

What's the next step from here, I can't run Samtools flagstat on my output file - this would be really useful as I'm trying to compare the % reads mapped using bowtie and stumpy.

Any insight would be hugely appreciated!

N