Pine tree

Links

• https://dendrome.ucdavis.edu/TGPlone
• http://www.pinegenome.org/pinerefseq

Data

• IPST ftp

 ftp genomepc1.umd.edu
 ftpuser
 pinegenome

 cd PineUpload052911/
 bin
 mget ...

• cChloroplast

 len     120481 
 gc%     38.55

• cBAC stats

 .       elem       min    q1     q2     q3     max        mean       n50        sum            
 len     102        8288   89909  116121 140549 172161     113400     126689     11566806       
 gc%     102        34.44  36.56  37.61  38.80  52.88      37.94      37.66      3870.87        

• Reads

                readLen   #mates
 FC638TR_001_8  146       22,729,231
 FC638TR_002_8  146       18,412,638

• Local data

 ginkgo:
 /scratch1/dpuiu/PINE/
 /scratch1/dpuiu/PINE/sample/        # 100K mates sampled from each lib
 /scratch1/dpuiu/PINE/sample/*stats

• Notes:
  • First 2bp of each read have higher A count
  • GC% variation:

                medianGC% 
 cChloroplast   38.55
 cBAC           37.61
 reads          39.04

Sampled data

• 100K sampled reads from each library (2*2*100K=400K)

 .       elem       min    q1     q2     q3     max        mean       n50        sum            
 gc%     400000     0.68   34.93  39.04  43.15  95.89      39.20      40.41      .

• FC638TR_001 : 100K reads

 ref            aligner      #hits      %hits
 cBAC           bwa bwasw    42971      43%
                nucmer       12477      12.5%
                bowtie       1186       1.2%

 cChloroplast   bwa bwasw    2031       2%
                nucmer       1943       1.9%
                bowtie       1490       1.5%