基因数据处理63之snap修改默认设置后处理大于400bp的记录

通过修改Read.h中的400=》4000，之后可以运行，但是匹配的命中率好低。但是bwamen很不错，下一篇有记录。

xubo@xubo:~/xubo/data/alignment/cs-bwamem$ snap-aligner single snapindex/ g38l500N10000.fq -o g38l500N10000.snap1.sam
Welcome to SNAP version 1.0beta.23.

Loading index from directory... 32s.  248957422 bases, seed size 20
Aligning.
Total Reads    Aligned, MAPQ >= 10    Aligned, MAPQ < 10     Unaligned              Too Short/Too Many Ns     Reads/s   Time in Aligner (s)
10,000         8,933 (89.33%)         98 (0.98%)             969 (9.69%)            0 (0.00%)                 4,068     2
xubo@xubo:~/xubo/data/alignment/cs-bwamem$ snap-aligner single snapindex/ g38l1000N10000.fq -o g38l1000N10000.snap1.sam
Welcome to SNAP version 1.0beta.23.

Loading index from directory... 33s.  248957422 bases, seed size 20
Aligning.
Total Reads    Aligned, MAPQ >= 10    Aligned, MAPQ < 10     Unaligned              Too Short/Too Many Ns     Reads/s   Time in Aligner (s)
10,000         796 (7.96%)            8 (0.08%)              9,196 (91.96%)         0 (0.00%)                 2,608     4

xubo@xubo:~/xubo/data/alignment/cs-bwamem$ snap-aligner snapindex/ g38l500N100000.fq -o g38l500N100000.snap.sam
Welcome to SNAP version 1.0beta.23.

Invalid command: snapindex/

Usage: snap-aligner <command> [<options>]
Commands:
   index    build a genome index
   single   align single-end reads
   paired   align paired-end reads
   daemon   run in daemon mode--accept commands remotely
Type a command without arguments to see its help.
xubo@xubo:~/xubo/data/alignment/cs-bwamem$ snap-aligner single  snapindex/ g38l500N100000.fq -o g38l500N100000.snap.sam
Welcome to SNAP version 1.0beta.23.

Loading index from directory... 34s.  248957422 bases, seed size 20
Aligning.
Total Reads    Aligned, MAPQ >= 10    Aligned, MAPQ < 10     Unaligned              Too Short/Too Many Ns     Reads/s   Time in Aligner (s)
100,000        88,891 (88.89%)        1,083 (1.08%)          10,026 (10.03%)        0 (0.00%)                 4,200     24

xubo@xubo:~/xubo/data/alignment/cs-bwamem$ snap-aligner single snapindex/ g38l1000N100000.fq -o g38l1000N100000.snap1.sam
Welcome to SNAP version 1.0beta.23.

Loading index from directory... 33s.  248957422 bases, seed size 20
Aligning.
Total Reads    Aligned, MAPQ >= 10    Aligned, MAPQ < 10     Unaligned              Too Short/Too Many Ns     Reads/s   Time in Aligner (s)
100,000        7,786 (7.79%)          67 (0.07%)             92,145 (92.14%)        2 (0.00%)                 2,390     42
xubo@xubo:~/xubo/data/alignment/cs-bwamem$ snap-aligner single snapindex/ g38l1000N1000000.fq -o g38l1000N1000000.snap1.sam
Welcome to SNAP version 1.0beta.23.

Loading index from directory... 32s.  248957422 bases, seed size 20
Aligning.
Total Reads    Aligned, MAPQ >= 10    Aligned, MAPQ < 10     Unaligned              Too Short/Too Many Ns     Reads/s   Time in Aligner (s)
1,000,000      78,762 (7.88%)         602 (0.06%)            920,610 (92.06%)       26 (0.00%)                2,420     413

统计信息：

xubo@xubo:~/xubo/data/alignment/cs-bwamem$ samtools flagstat g38l500N10000.snap1.sam 
10000 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
9031 + 0 mapped (90.31% : N/A)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (N/A : N/A)
0 + 0 with itself and mate mapped
0 + 0 singletons (N/A : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
xubo@xubo:~/xubo/data/alignment/cs-bwamem$ samtools flagstat g38l500N100000.snap1.sam 
[E::hts_open_format] fail to open file 'g38l500N100000.snap1.sam'
samtools flagstat: Cannot open input file "g38l500N100000.snap1.sam": No such file or directory
xubo@xubo:~/xubo/data/alignment/cs-bwamem$ samtools flagstat g38l500N100000.snap.sam 
100000 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
89974 + 0 mapped (89.97% : N/A)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (N/A : N/A)
0 + 0 with itself and mate mapped
0 + 0 singletons (N/A : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
xubo@xubo:~/xubo/data/alignment/cs-bwamem$ samtools flagstat g38l1000N10000.snap1.sam 
10000 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
804 + 0 mapped (8.04% : N/A)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (N/A : N/A)
0 + 0 with itself and mate mapped
0 + 0 singletons (N/A : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
xubo@xubo:~/xubo/data/alignment/cs-bwamem$ samtools flagstat g38l1000N100000.snap1.sam 
100000 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
7853 + 0 mapped (7.85% : N/A)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (N/A : N/A)
0 + 0 with itself and mate mapped
0 + 0 singletons (N/A : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
xubo@xubo:~/xubo/data/alignment/cs-bwamem$ samtools flagstat g38l1000N1000000.snap1.sam 
1000000 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
79364 + 0 mapped (7.94% : N/A)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (N/A : N/A)
0 + 0 with itself and mate mapped
0 + 0 singletons (N/A : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
xubo@xubo:~/xubo/data/alignment/cs-bwamem$ 

参考

【1】https://github.com/xubo245/AdamLearning
【2】https://github.com/bigdatagenomics/adam/ 
【3】https://github.com/xubo245/SparkLearning
【4】http://spark.apache.org
【5】http://stackoverflow.com/questions/28166667/how-to-pass-d-parameter-or-environment-variable-to-spark-job  
【6】http://stackoverflow.com/questions/28840438/how-to-override-sparks-log4j-properties-per-driver

研究成果：

【1】 [BIBM] Bo Xu, Changlong Li, Hang Zhuang, Jiali Wang, Qingfeng Wang, Chao Wang, and Xuehai Zhou, "Distributed Gene Clinical Decision Support System Based on Cloud Computing", in IEEE International Conference on Bioinformatics and Biomedicine. (BIBM 2017, CCF B)
【2】 [IEEE CLOUD] Bo Xu, Changlong Li, Hang Zhuang, Jiali Wang, Qingfeng Wang, Xuehai Zhou. Efficient Distributed Smith-Waterman Algorithm Based on Apache Spark (CLOUD 2017, CCF-C).
【3】 [CCGrid] Bo Xu, Changlong Li, Hang Zhuang, Jiali Wang, Qingfeng Wang, Jinhong Zhou, Xuehai Zhou. DSA: Scalable Distributed Sequence Alignment System Using SIMD Instructions. (CCGrid 2017, CCF-C).
【4】more: https://github.com/xubo245/Publications

Help

If you have any questions or suggestions, please write it in the issue of this project or send an e-mail to me: xubo245@mail.ustc.edu.cn
Wechat: xu601450868
QQ: 601450868