| Line 8: |
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pacBioToCA -l viaMiseq -s pacbio.spec -t 10 -partitions 200 fastqFile=m120228_192221.fastq genomeSize=4650000 ../../tMiSeq_PE.frg |
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pacBioToCA -l viaMiseq -s pacbio.spec -t 10 -partitions 200 fastqFile=m120228_192221.fastq genomeSize=4650000 ../../tMiSeq_PE.frg |
| |
|
|
|
| - |
m120228_192221_42129_c100298890010000001523009207231260_s1_p0.fastq
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+ |
m120228_192221_42129_c100298890010000001523009207231260_s1_p0.fastq<br>
|
| - |
seqs amount:38542
|
+ |
seqs amount:38542<br>
|
| - |
seq avg len:2322.679985
|
+ |
seq avg len:2322.679985<br>
|
| - |
total:89.52 Mb
|
+ |
total:89.52 Mb<br>
|
| - |
depth: 19.25X
|
+ |
depth: 19.25X<br>
|
| |
|
+ |
<br>
|
| - |
(without genomeSize)PacBio_Illumia.fasta
|
+ |
(without genomeSize)PacBio_Illumia.fasta<br>
|
| - |
seqs amount:34981
|
+ |
seqs amount:34981<br>
|
| - |
seq avg len:2133.783826
|
+ |
seq avg len:2133.783826<br>
|
| - |
total:74.64 Mb
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+ |
total:74.64 Mb<br>
|
| - |
depth: 16.05X
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+ |
depth: 16.05X<br>
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| |
|
+ |
<br>
|
| - |
4650000
|
+ |
4650000<br>
|
| - |
viaMiseq.fasta
|
+ |
(with genomeSize)viaMiseq.fasta<br>
|
| - |
seqs amount:34852
|
+ |
seqs amount:34852<br>
|
| - |
seq avg len:2130.841559
|
+ |
seq avg len:2130.841559<br>
|
| - |
total:74.26 Mb
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+ |
total:74.26 Mb<br>
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| - |
depth: 15.97X => 看起來在只有一組的情況下，沒有差很多
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+ |
depth: 15.97X => 看起來在只有一組的情況下，沒有差很多<br>
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+ |
<br>
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==Random Get Two== |
|
==Random Get Two== |
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pacBioToCA -l viaMiseq -s pacbio.spec -t 10 -partitions 200 fastqFile=Filtered_two.fastq genomeSize=4650000 ../tMiSeq_PE.frg |
|
pacBioToCA -l viaMiseq -s pacbio.spec -t 10 -partitions 200 fastqFile=Filtered_two.fastq genomeSize=4650000 ../tMiSeq_PE.frg |
| - |
Filtered_two.fastq
|
+ |
<br>
|
| - |
seqs amount:77117
|
+ |
Filtered_two.fastq<br>
|
| - |
seq avg len:2184.208709
|
+ |
seqs amount:77117<br>
|
| - |
total:168.44 Mb
|
+ |
seq avg len:2184.208709<br>
|
| - |
depth: 36.22X
|
+ |
total:168.44 Mb<br>
|
| |
|
+ |
depth: 36.22X<br>
|
| - |
(without genomeSize)PacBio_Illumia.fasta
|
+ |
<br>
|
| - |
seqs amount:63760
|
+ |
(without genomeSize)PacBio_Illumia.fasta<br>
|
| - |
seq avg len:2199.845561
|
+ |
seqs amount:63760<br>
|
| - |
total:140.26 Mb
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+ |
seq avg len:2199.845561<br>
|
| - |
depth: 30.16X
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+ |
total:140.26 Mb<br>
|
| |
|
+ |
depth: 30.16X<br>
|
| - |
4650000
|
+ |
<br>
|
| - |
viaMiseq.fasta
|
+ |
4650000<br>
|
| - |
seqs amount:63411
|
+ |
(with genomeSize)viaMiseq.fasta<br>
|
| - |
seq avg len:2198.455315
|
+ |
seqs amount:63411<br>
|
| - |
total:139.41 Mb
|
+ |
seq avg len:2198.455315<br>
|
| - |
depth: 29.98X => 看起來在只有二組的情況下，沒有差很多
|
+ |
total:139.41 Mb<br>
|
| |
|
+ |
depth: 29.98X => 看起來在只有二組的情況下，沒有差很多<br>
|
| |
|
+ |
<br>
|
| |
==Random Get Three== |
|
==Random Get Three== |
| |
pacBioToCA -l viaMiseq -s pacbio.spec -t 10 -partitions 200 fastqFile=Filtered_three.fastq genomeSize=4650000 ../tMiSeq_PE.frg |
|
pacBioToCA -l viaMiseq -s pacbio.spec -t 10 -partitions 200 fastqFile=Filtered_three.fastq genomeSize=4650000 ../tMiSeq_PE.frg |
| - |
Filtered_three.fastq
|
|
|
| - |
seqs amount:113284
|
|
|
| - |
seq avg len:2333.977711
|
|
|
| - |
total:264.40 Mb
|
|
|
| - |
depth: 56.86X
|
|
|
| |
|
|
|
| - |
PacBio_Illumia.fasta
|
+ |
Filtered_three.fastq<br>
|
| - |
seqs amount:98165
|
+ |
seqs amount:113284<br>
|
| - |
seq avg len:2286.482249
|
+ |
seq avg len:2333.977711<br>
|
| - |
total:224.45 Mb
|
+ |
total:264.40 Mb<br>
|
| - |
depth: 48.27X
|
+ |
depth: 56.86X<br>
|
| |
|
+ |
<br>
|
| - |
4650000
|
+ |
(without genomeSize)PacBio_Illumia.fasta<br>
|
| - |
viaMiseq.fasta
|
+ |
seqs amount:98165<br>
|
| - |
seqs amount:70468
|
+ |
seq avg len:2286.482249<br>
|
| - |
seq avg len:2815.903020
|
+ |
total:224.45 Mb<br>
|
| - |
total:198.43 Mb
|
+ |
depth: 48.27X<br>
|
| - |
depth: 42.67X => 看起來要有三組以上的的情況下，genomeSize才有效果。
|
+ |
<br>
|
| |
|
+ |
4650000<br>
|
| |
|
+ |
(with genomeSize)viaMiseq.fasta<br>
|
| |
|
+ |
seqs amount:70468<br>
|
| |
|
+ |
seq avg len:2815.903020<br>
|
| |
|
+ |
total:198.43 Mb<br>
|
| |
|
+ |
depth: 42.67X => 看起來要有三組以上的的情況下，genomeSize才有效果。<br>
|
| |
|
+ |
<br>
|
| |
==Random Get Four== |
|
==Random Get Four== |
| |
pacBioToCA -l viaMiseq -s pacbio.spec -t 10 -partitions 200 fastqFile=Filtered_four.fastq genomeSize=4650000 ../tMiSeq_PE.frg |
|
pacBioToCA -l viaMiseq -s pacbio.spec -t 10 -partitions 200 fastqFile=Filtered_four.fastq genomeSize=4650000 ../tMiSeq_PE.frg |
| - |
Filtered_four.fastq
|
|
|
| - |
seqs amount:136333
|
|
|
| - |
seq avg len:2386.664674
|
|
|
| - |
total:325.38 Mb
|
|
|
| - |
depth: 69.97X
|
|
|
| |
|
|
|
| - |
PacBio_Illumia.fasta
|
+ |
Filtered_four.fastq<br>
|
| - |
seqs amount:118901
|
+ |
seqs amount:136333<br>
|
| - |
seq avg len:2320.548322
|
+ |
seq avg len:2386.664674<br>
|
| - |
total:275.92 Mb
|
+ |
total:325.38 Mb<br>
|
| - |
depth: 59.34X
|
+ |
depth: 69.97X<br>
|
| |
|
+ |
<br>
|
| - |
4650000
|
+ |
(without genomeSize)PacBio_Illumia.fasta<br>
|
| - |
viaMiseq.fasta
|
+ |
seqs amount:118901<br>
|
| - |
seqs amount:56298
|
+ |
seq avg len:2320.548322<br>
|
| - |
seq avg len:3495.604515
|
+ |
total:275.92 Mb<br>
|
| - |
total:196.80 Mb
|
+ |
depth: 59.34X<br>
|
| - |
depth: 42.32X => 看起來要有三組以上的的情況下，genomeSize才有效果。
|
+ |
<br>
|
| |
|
+ |
4650000<br>
|
| |
|
+ |
(with genomeSize)viaMiseq.fasta<br>
|
| |
|
+ |
seqs amount:56298<br>
|
| |
|
+ |
seq avg len:3495.604515<br>
|
| |
|
+ |
total:196.80 Mb<br>
|
| |
|
+ |
depth: 42.32X => 看起來要有三組以上的的情況下，genomeSize才有效果。<br>
|
| |
|
+ |
<br>
|
| |
|
|
|
| |
= runCA = |
|
= runCA = |
