Barcode Name	Sample	Bases	>=Q20 Bases	Reads	Mean Read Length
No barcode	None	324883423	231528034	3023221	107 bp 
IonXpressRNA_011	GKR11-wt3late	5126340137	4202745112	43112235	118 bp 
IonXpressRNA_012	GKR12-DARE3late	5262496686	4305617191	44141947	119 bp 

GKlab_12RNAseq_GKR11r-wt3late-bc11_GKR12r-DARE3late-bc12

../rnaSeq-pip4fast-mm9-solid.sh

Reads:
          Input     :  43112235
           Mapped   :  24573057 (57.0% of input)
            of these:    897068 ( 3.7%) have multiple alignments (22173 have >20)
57.0% overall read mapping rate.

18539178 reads; of these:
  18539178 (100.00%) were unpaired; of these:
    1715855 (9.26%) aligned 0 times
    5914149 (31.90%) aligned exactly 1 time
    10909174 (58.84%) aligned >1 times
90.74% overall alignment rate
40965050 uniq. mapped reads
(/ 40965050 43112235.0)
0.9501954607549342


Reads:
          Input     :  44141947
           Mapped   :  23571826 (53.4% of input)
            of these:    943486 ( 4.0%) have multiple alignments (21695 have >20)
53.4% overall read mapping rate.
20570121 reads; of these:
  20570121 (100.00%) were unpaired; of these:
    1665602 (8.10%) aligned 0 times
    5931301 (28.83%) aligned exactly 1 time
    12973218 (63.07%) aligned >1 times
91.90% overall alignment rate
42063858 uniq. mapped reads
(/ 42063858 44141947.0)
0.9529225795137672