This thread comes from http://seqanswers.com/forums/showthread.php?t=6820 but I prefer to start a new one becase there it was a little off topic.
I have two samples, from 2 different patients with the same diagnosed illness, procesed with the same protocol. Each sample is composed by a pair of files that I must merge. With one sample I get some merging but with the other I get almost nothing.
Let me show you results:
HIGH MERGING case
java -Djava.library.path=/home/carlos/BBMap/bbmap/jni/ -ea -Xmx1000m -cp /home/carlos/BBMap/bbmap/current/ jgi.BBMerge in1=high_merge_R1.fq in2=high_merge_R2.fq out=merged.fastq outu1=unmerged1.fastq outu2=unmerged2.fastq
Executing jgi.BBMerge [in1=high_merge_R1.fq, in2=high_merge_R2.fq, out=merged.fastq, outu1=unmerged1.fastq, outu2=unmerged2.fastq]
BBMerge version 8.8
Writing mergable reads merged.
Started output threads.
Total time: 14,914 seconds.
Pairs: 141970
Joined: 83109 58,540%
Ambiguous: 50033 35,242%
No Solution: 8828 6,218%
Too Short: 0 0,000%
Avg Insert: 156,0
Standard Deviation: 18,5
Mode: 149
Insert range: 63 - 291
90th percentile: 197
75th percentile: 152
50th percentile: 150
25th percentile: 148
10th percentile: 145
LOW MERGING case
java -Djava.library.path=/home/carlos/BBMap/bbmap/jni/ -ea -Xmx1000m -cp /home/carlos/BBMap/bbmap/current/ jgi.BBMerge in1=low_merge_R1.fq in2=low_merge_R2.fq out=merged.fastq outu1=unmerged1.fastq outu2=unmerged2.fastq
Executing jgi.BBMerge [in1=low_merge_R1.fq, in2=low_merge_R2.fq, out=merged.fastq, outu1=unmerged1.fastq, outu2=unmerged2.fastq]
BBMerge version 8.8
Writing mergable reads merged.
Started output threads.
Total time: 49,182 seconds.
Pairs: 548979
Joined: 140 0,026%
Ambiguous: 548807 99,969%
No Solution: 32 0,006%
Too Short: 0 0,000%
Avg Insert: 122,8
Standard Deviation: 64,3
Mode: 126
Insert range: 36 - 592
90th percentile: 193
75th percentile: 156
50th percentile: 126
25th percentile: 63
10th percentile: 49
I have two samples, from 2 different patients with the same diagnosed illness, procesed with the same protocol. Each sample is composed by a pair of files that I must merge. With one sample I get some merging but with the other I get almost nothing.
Let me show you results:
HIGH MERGING case
java -Djava.library.path=/home/carlos/BBMap/bbmap/jni/ -ea -Xmx1000m -cp /home/carlos/BBMap/bbmap/current/ jgi.BBMerge in1=high_merge_R1.fq in2=high_merge_R2.fq out=merged.fastq outu1=unmerged1.fastq outu2=unmerged2.fastq
Executing jgi.BBMerge [in1=high_merge_R1.fq, in2=high_merge_R2.fq, out=merged.fastq, outu1=unmerged1.fastq, outu2=unmerged2.fastq]
BBMerge version 8.8
Writing mergable reads merged.
Started output threads.
Total time: 14,914 seconds.
Pairs: 141970
Joined: 83109 58,540%
Ambiguous: 50033 35,242%
No Solution: 8828 6,218%
Too Short: 0 0,000%
Avg Insert: 156,0
Standard Deviation: 18,5
Mode: 149
Insert range: 63 - 291
90th percentile: 197
75th percentile: 152
50th percentile: 150
25th percentile: 148
10th percentile: 145
LOW MERGING case
java -Djava.library.path=/home/carlos/BBMap/bbmap/jni/ -ea -Xmx1000m -cp /home/carlos/BBMap/bbmap/current/ jgi.BBMerge in1=low_merge_R1.fq in2=low_merge_R2.fq out=merged.fastq outu1=unmerged1.fastq outu2=unmerged2.fastq
Executing jgi.BBMerge [in1=low_merge_R1.fq, in2=low_merge_R2.fq, out=merged.fastq, outu1=unmerged1.fastq, outu2=unmerged2.fastq]
BBMerge version 8.8
Writing mergable reads merged.
Started output threads.
Total time: 49,182 seconds.
Pairs: 548979
Joined: 140 0,026%
Ambiguous: 548807 99,969%
No Solution: 32 0,006%
Too Short: 0 0,000%
Avg Insert: 122,8
Standard Deviation: 64,3
Mode: 126
Insert range: 36 - 592
90th percentile: 193
75th percentile: 156
50th percentile: 126
25th percentile: 63
10th percentile: 49
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