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=== Paired-End reads === * We must use some kind of PE reads stitching software to combine R1 and R2. However, whenever we do that, the forward and reverse strand correlation always show poorer data quality than when using only R1 or R2 data alone. I've tested COPE and PEAR on GP1V4 capture data where 99% of all paired end reads were overlapping with PE 150 reads, but the results were always bad. So I decided that clipping overlap in the BAM files would be better than stitching PE reads together since all the models for stitching seems to be based on non-bisulfite data (for genome assembly purposes.) * BamUtils have clipOverlap module that I can use for clipping, but must correctly flag all paired reads in BAM files for this to work. http://genome.sph.umich.edu/wiki/BamUtil#Releases * I incorporated this step into BamExtractor module for BisReadMapper so there is no need to perform stitching in the future. * Note tha BamUtils clipOverlap will only perform soft-clip, so the clipping is only indicated in the CIGAR string but not performed on the actual sequence. * clipOverlap also guarantees that any overlapping PE reads will get trimmed while stitching program may fail to perform stitching on some overlapping PEs. {| class="wikitable" | align="center" style="background:#f0f0f0;"|'''Sample File''' | align="center" style="background:#f0f0f0;"|'''Read 1 only''' | align="center" style="background:#f0f0f0;"|'''Read 2 only''' | align="center" style="background:#f0f0f0;"|'''COPE''' | align="center" style="background:#f0f0f0;"|'''PEAR''' | align="center" style="background:#f0f0f0;"|'''clipOverlap''' |- | NP-GP1V4-Ind1-16-Dec26-Ind1_S1||N=2140, r=0.944999843530629||N=1956, r=0.948678833946809||N=4493, r=0.905426295537918||N=4575, r=0.880593815314892||N=3766, r=0.947693618322778 |- | NP-GP1V4-Ind1-16-Dec26-Ind2_S2||N=1307, r=0.947753281327104||N=1309, r=0.919215799033252||N=3292, r=0.872723283319447||N=3004, r=0.853236631821437||N=2627, r=0.930015463563508 |- | NP-GP1V4-Ind1-16-Dec26-Ind3_S3||N=1238, r=0.923621136109205||N=1049, r=0.896750712776968||N=2892, r=0.877732324287496||N=2630, r=0.846694242580542||N=2340, r=0.918090849213536 |- | NP-GP1V4-Ind1-16-Dec26-Ind4_S4||N=1410, r=0.965669325893385||N=1324, r=0.954974476737397||N=3182, r=0.90491763432851||N=3022, r=0.861150327721996||N=2674, r=0.958392440240385 |- | NP-GP1V4-Ind1-16-Dec26-Ind5_S5||N=1437, r=0.895241800627052||N=1272, r=0.833958253713675||N=3468, r=0.82057943147337||N=3109, r=0.779392712114823||N=2839, r=0.858475255821648 |- | NP-GP1V4-Ind1-16-Dec26-Ind6_S6||N=1114, r=0.915859349526694||N=963 , r=0.932666798629509||N=2459, r=0.753298536985006||N=2254, r=0.678976136765023||N=1994, r=0.914004826333877 |- | NP-GP1V4-Ind1-16-Dec26-Ind7_S7||N=458 , r=0.853321515878049||N=340 , r=0.892339454612493||N=1178, r=0.692036233842428||N=766 , r=0.570623971432356||N=896 , r=0.800442726207723 |- | NP-GP1V4-Ind1-16-Dec26-Ind8_S8||N=775 , r=0.923504016994822||N=581 , r=0.924650338321257||N=1809, r=0.760451037849||N=1432, r=0.654256010151288||N=1430, r=0.898359952429347 |}
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