R-Rsolid-0.9.31-20.fc26$>_Rb7WS>:#?#d   h $HL[jw H   8    4 Bp   (89:;GLHI<X\Yd\]^ b d e f l t!u!|v!w"x#,y###CR-Rsolid0.9.3120.fc26Quantile normalization and base calling for second generation sequencing data Rsolid is an R package for normalizing fluorescent intensity data from ABI/SOLiD second generation sequencing platform. It has been observed that the color-calls provided by factory software contain technical artifacts, where the proportions of colors called are extremely variable across sequencing cycles. Under the random DNA fragmentation assumption, these proportions should be equal across sequencing cycles and proportional to the dinucleotide frequencies of the sample. Rsolid implements a version of the quantile normalization algorithm that transforms the intensity values before calling colors. Results show that after normalization, the total number of mappable reads increases by around 5%, and number of perfectly mapped reads increases by 10%. Moreover a 2-5% reduction in overall error rates is observed, with a 2-6% reduction in the rate of valid adjacent color mis-matches. The latter is important, since it leads to a decrease in false-positive SNP calls. The normalization algorithm is computationally efficient. In a test we are able to process 300 million reads in 2 hours using 10 computer cluster nodes. The engine functions of the package are written in C for better performance.Y.ɐbuildvm-06.phx2.fedoraproject.orgEFedora ProjectFedora ProjectArtistic 2.0Fedora ProjectApplications/Engineeringhttp://rafalab.jhsph.edu/Rsolid/linuxx86_64Gn.dz @a Cc7 k A큤A큤A큤A큤A큤A큤AY.ɇY.ɆY.ɇY.ɇY.ɇY.ɇY.ɆY.ɇY.ɇY.ɇY.ɆY.ɆY.ɇY.ɇY.ɇY.ɇY.ɇY.ɇY.ɇY.ɇY.ɇY.ɇY.ɇY.ɇY.ɇY.ɇY.ɇY.ɇY.ɇY.ɇ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-Rsolid-0.9.31-20.fc26.src.rpmR-RsolidR-Rsolid(x86-64) @@@@@@@    @R-corelibR.so()(64bit)libc.so.6()(64bit)libc.so.6(GLIBC_2.14)(64bit)libc.so.6(GLIBC_2.2.5)(64bit)libc.so.6(GLIBC_2.3.4)(64bit)libc.so.6(GLIBC_2.4)(64bit)libhdf5.so.10()(64bit)rpmlib(CompressedFileNames)rpmlib(FileDigests)rpmlib(PayloadFilesHavePrefix)rpmlib(PayloadIsXz)rtld(GNU_HASH)3.4.03.0.4-14.6.0-14.0-15.2-14.13.0.1Y.@X@VV@UUXTS@S@Q@Q@Qg@Q@P@O@Nk@M@Mc@MOLrbLZL@IL@IL;L3L@Tom Callaway - 0.9.31-20Fedora Release Engineering - 0.9.31-19Fedora Release Engineering - 0.9.31-18Orion Poplawski - 0.9.31-17Fedora Release Engineering - 0.9.31-16Orion Poplawski - 0.9.31-15Orion Poplawski - 0.9.31-14Fedora Release Engineering - 0.9.31-13Fedora Release Engineering - 0.9.31-12Fedora Release Engineering - 0.9.31-11Orion Poplawski - 0.9.31-10Tom Callaway - 0.9.31-9Fedora Release Engineering - 0.9.31-8Fedora Release Engineering - 0.9.31-7Fedora Release Engineering - 0.9.31-6Tom Callaway - 0.9.31-5Adam Huffman - 0.9.31-4Orion Poplawski - 0.9.31-3Fedora Release Engineering - 0.9.31-2Adam Huffman - 0.9.31-1Adam Huffman - 0.9.3-1Adam Huffman - 0.9.2-4Adam Huffman - 0.9.2-3Adam Huffman - 0.9.2-2Adam Huffman - 0.9.2-1Adam Huffman - 0.9.1-1- rebuild for R 3.4.0- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild- Rebuild for hdf5 1.8.16- Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild- Rebuild for hdf5 1.8.15- Rebuild for hdf5 1.8.14- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild- Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild- Rebuild for hdf5 1.8.11- rebuild for R3- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild- Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild- Rebuilt for https://fedoraproject.org/wiki/Fedora_17_Mass_Rebuild- rebuild for R 2.14.0- remove executable files to pass check- Rebuild for hdf5 1.8.7- Rebuilt for https://fedoraproject.org/wiki/Fedora_15_Mass_Rebuild- another upstream bugfix release- New upstream bugfix release- fix duplicated files entries- new upstream release with licensing clarification - specfile cleanups to address reviewer comments: - directory ownership - requires- spec formatting cleanups- new release with ability to disable bundled HDF5 - fix files section - -devel subpackage- initial package for Fedora 0.9.31-20.fc260.9.31-20.fc26RsolidDESCRIPTIONINDEXMetaRd.rdsdata.rdsfeatures.rdshsearch.rdslinks.rdsnsInfo.rdspackage.rdsNAMESPACERRsolidRsolid.rdbRsolid.rdxdataprop.Hs.rdahelpAnIndexRsolid.rdbRsolid.rdxaliases.rdspaths.rdshtml00Index.htmlR.cssRsolid.htmllibsRsolid.so/usr/lib64/R/library//usr/lib64/R/library/Rsolid//usr/lib64/R/library/Rsolid/Meta//usr/lib64/R/library/Rsolid/R//usr/lib64/R/library/Rsolid/data//usr/lib64/R/library/Rsolid/help//usr/lib64/R/library/Rsolid/html//usr/lib64/R/library/Rsolid/libs/-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=genericdrpmxz2x86_64-redhat-linux-gnudirectoryASCII textHTML document, ASCII textELF 64-bit LSB shared object, x86-64, version 1 (SYSV), dynamically linked, BuildID[sha1]=342b85fbc1f6ae24abb8751abf353fee904289b3, strippedRRRRRRRR utf-8?`7zXZ !#,G7i]"k%j1&qB]HHƥ ș&k+JeCޓfFoT=8'B EbR7!d|VOV4y*]؎D9oC]Hsځϫrkqf:2[U[yT+png#8 !!JV;\{w^B;Yq? li~Hyv'A= [`5fTH[@\3P缧vtBVqiRM1CH9K("`#b oD)]q8$yr-Avp|/Mc ٽ(!A0 " Y5_p|,҅<ʹes7 ֶfnÎ{ ҕWDǏ=L"El8%8xzE5ߦ[{cLD 44NU-3`fA2Յ+Bwk n;n_\&@%AOC9N/ӟ&EFaXV(oqJmrh m^/MU<X<Ú*`{6Gf1jD{ [/{Z8ߙ&Ư-$٭$]C3n01 [0(?P_\@Põ^ JJPœr jARQlJ3ASyI Z}}(`?acpy˟V1e{Mc5Qw6'nq '<?k͙dcy쎷l)n l) v~ y{w!N~Ai)GQ;̑T~xٍd: 3=GvQ6jx#gM%Q?_L7+9\`Ysږx)%oN1u ޡڣX4*YkR.o+eqՆLgfl˶. 87ewη7? !Gy>;`"iz7v'E=#>$ἰm>mZi9hE>ՅJOm nkKuJ&^?"7'pfUQ EyOgg *4(3̙2Fd_;+@:W_{亵kl+&s~8 X]}@pj)bX]JUby^!(\//HC|FWJ@PM 93"3K~aչ'o#Q!:nhW`lzr9.@bi#}U5o ]"uŸ= bXc:U$g: fd>H[: mT[0lgIQ)\9[[n!`#'&_3oD+>zMa;Āᾩu- pCːf-r J:h]jtMZNS;tLA rΒ 2&+Vx”^x^y&*.i<ɛ[6!_=Gz7͛s\Hw5oa uߞ}4':û7 ÉzX6!oyJil n^z_جF|Ҧ= Wk?)VP廌95n汒BkIa=$+263Hrd=;S9D~'cgC^W(F}Qz~O 7U6r_pԒ*m *5!<0egHcT!T`ei%wT.UQ}G{j;yO:=R9ؔllNXJ`2!Q I>] l8~@AB`ܽ+mzsg\z:>^*,0 4+L)c3=ձŪuDlPh1{4NWwuK7a=GĂ`o3Ls{CP q*Of2:!Eohs`iQa w٨é5 .[wu2s᭟Nj*A=E1dUҏ`jm*̊s m}X9pYGu4;S( M5k\> &j'y`=(DKK*o "!'Vd 8'[nViverP=-9*Uܯ@6ooQBn]վXp `TU舭Hډ֘](C/_fcA_\\T;duㅹmb,X@nz6Hc `;#SV.NqL#xE/Y[\Ru際r`uvtV.M1+o9u0J4  usbta_y:﷣*/KfI#_+\'.EZ8kökP՞&eUXU9A@3gWrөM\90w@{_)jLT=ml@"%.s<so9iA(5Xl\ZrMdϭ9 .s#Q%=#hm(uI!0|eڻq;3 Gdj@hF3[$t?ֆ^y+n9=DE':> MIC͉:]"E &*WmpTdKP)$#oDdF!ɦivF# T^ |~M4;xIB(rƛyja:s@(,lkPVI֫ͧIMXwaxi[OvmrwRբpq]oEu]:]+٘7qoٙ%l!*?qm ՜ը&rlԙ=?`wrnj䮏|N"R4,F]ۢrk/oc_.f۬@=xQ@3KÞQlMDj}pV>!s{O}o@Denld9_*! 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