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| = Citing QPLOT = | | = Citing QPLOT = |
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− | If you found QPLOT useful and wants to cite in your paper, please refer to the information below. | + | If you found QPLOT useful and wants to cite in your paper, please copy and paste the information below. |
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− | Bingshan Li, Xiaowei Zhan, Mary-Kate Wing, Paul Anderson, Hyun Min Kang, and Goncalo R. Abecasis, “QPLOT: A Quality Assessment Tool for Next Generation Sequencing Data,” BioMed Research International, vol. 2013, Article ID 865181, 4 pages, 2013. doi:10.1155/2013/865181 http://www.hindawi.com/journals/bmri/2013/865181/
| + | * Bingshan Li, Xiaowei Zhan, Mary-Kate Wing, Paul Anderson, Hyun Min Kang, and Goncalo R. Abecasis, “QPLOT: A Quality Assessment Tool for Next Generation Sequencing Data,” BioMed Research International, vol. 2013, Article ID 865181, 4 pages, 2013. doi:10.1155/2013/865181 http://www.hindawi.com/journals/bmri/2013/865181/ |
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| = Where to Find It = | | = Where to Find It = |
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| == Binary Download == | | == Binary Download == |
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− | We have prepared a pre-compiled (under Ubuntu) qplot along with source code . You can download it from: [http://www.sph.umich.edu/csg/zhanxw/software/qplot/qplot.20130627.tar.gz qplot.20130627.tar.gz (File Size: 1.7G)] | + | We have prepared a pre-compiled (under Ubuntu) qplot along with source code . You can download it from: [http://csg.sph.umich.edu//zhanxw/software/qplot/qplot.20130627.tar.gz qplot.20130627.tar.gz (File Size: 1.7G)] |
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| The executable file is under qplot/bin/qplot. | | The executable file is under qplot/bin/qplot. |
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| == Source Code Distribution == | | == Source Code Distribution == |
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− | We provide a source code only download in [http://www.sph.umich.edu/csg/zhanxw/software/qplot/qplot-source.20130627.tar.gz qplot-source.20130627.tar.gz]. Optionally, you can download example file and/or data file: | + | We provide a source code only download in [http://csg.sph.umich.edu//zhanxw/software/qplot/qplot-source.20130627.tar.gz qplot-source.20130627.tar.gz]. Optionally, you can download example file and/or data file: |
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− | [http://www.sph.umich.edu/csg/zhanxw/software/qplot/qplot-example.tar.gz example]: example input file, and expected outputs if you following the [[#Built-in example | direction]]. | + | [http://csg.sph.umich.edu//zhanxw/software/qplot/qplot-example.tar.gz example]: example input file, and expected outputs if you following the [[#Built-in example | direction]]. |
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− | [http://www.sph.umich.edu/csg/zhanxw/software/qplot/qplot-data.tar.gz resources data]: necessary input files for qplot, including NCBI human genome build v37, dbSNP 130, and pre-computed GC file with windows size 100. | + | [http://csg.sph.umich.edu//zhanxw/software/qplot/qplot-data.tar.gz resources data]: necessary input files for qplot, including NCBI human genome build v37, dbSNP 130, and pre-computed GC file with windows size 100. |
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| You can put above file(s) in the same folder and follow these steps: | | You can put above file(s) in the same folder and follow these steps: |
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| or | | or |
| --qcfail_keep | | --qcfail_keep |
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| *Records to process | | *Records to process |
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| '''NOTE''' In order for this to work, the lane info has to be encoded in the read name such that the lane number is the second field with the delimiter ":". | | '''NOTE''' In order for this to work, the lane info has to be encoded in the read name such that the lane number is the second field with the delimiter ":". |
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| * Read group to process : | | * Read group to process : |
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− | Read group option can restrict qplot to process a subset of reads. For example, if BAM contain the following @RG tags:
| + | The read group option can restrict qplot to process a subset of reads. For example, if the BAM contains the following @RG tags: |
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| @RG ID:UM0348_1:1 PL:ILLUMINA LB:M5390 SM:M5390 CN:UM | | @RG ID:UM0348_1:1 PL:ILLUMINA LB:M5390 SM:M5390 CN:UM |
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| @RG ID:UM0360_4:1 PL:ILLUMINA LB:M5390 SM:M5390 CN:UM | | @RG ID:UM0360_4:1 PL:ILLUMINA LB:M5390 SM:M5390 CN:UM |
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− | If specify nothing or not using "--readGroup", QPLOT by default will process all reads;
| + | QPLOT will by default (without specifying --readgroup) process all reads. |
− | If specify "--readGroup UM0348", then only read group UM0348_1, UM_0348_2, UM_0348_3, UM_0348_4 will be processed; | + | |
− | If specify "--readGroup UM0348_1", then only one read group UM0348_1 will be processed. | + | If you specify "--readGroup UM0348", then only read groups UM0348_1, UM_0348_2, UM_0348_3, UM_0348_4 will be processed. |
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| + | If you specify "--readGroup UM0348_1", then only one read group, UM0348_1, will be processed. |
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| * Input file options : | | * Input file options : |
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− | BAM files are compress by BGZF algorithm and it should contain EOF by default. QPLOT will by default stop working when it does not found a valid EOF tag inside BAM files. | + | BAM files are compressed using BGZF and should contain the EOF indicator by default. QPLOT will, by default, stop working if it does not find a valid EOF indicator inside the BAM files. |
− | However, you can force QPLOT to continue process using --noeof. But you should be aware the input files may be corrupted. | + | However, you can force QPLOT to continue processing BAM files without an EOF indicator using --noeof. But you should be aware the input files may be corrupted. |
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| Qplot will exclude reads with lower mapping qualities than the user specified parameter, <code>--minMapQuality</code>. By default, mapped reads with all mapping quality will be included in the analysis. | | Qplot will exclude reads with lower mapping qualities than the user specified parameter, <code>--minMapQuality</code>. By default, mapped reads with all mapping quality will be included in the analysis. |
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| *Region list | | *Region list |