Hi,
I want to try MAQ (for the first time) for analysis of Illumina HiSeq human whole exome results, and I have two questions:
1. Is it ok to use hg19_chromFa.tar (from UCSC) as a reference, or should I run it again each chromosome individually ?
2. The text file I got from the HiSeq (which is fastq actually) is ok as an input for maq fasta2bfa command, or should I change its fastq format? I think that Hiseq output is already in the Sanger fastq format, but I'm not sure? below I copied the beginning of the txt file.
Thanks!
@ILLUMINA-FFC6C4_0005:7:1:1941:1087#0/1
CACATTGGATTGATCGGTCTCATTGGCCCCCCGGGAGAAGCTGGGGAGAAAGGAGATCAGGGGGTGCCAGGCGT
+ILLUMINA-FFC6C4_0005:7:1:1941:1087#0/1
faf\f_ccfffffSedaRe\dcdYffffcggg`g^ae`ca^RbaJ_VWW_Z\\Na`d``]a`bGM[UYVa`]`B
@ILLUMINA-FFC6C4_0005:7:1:2045:1092#0/1
GTGTGAATTTCATTTCCACATAAATTTTCTGAGCTGCATCACGGGAGATCCAGTTTGTACGAAGCCAGTTGTTT
+ILLUMINA-FFC6C4_0005:7:1:2045:1092#0/1
fffff_ffff[a\feaacafffffgfggcff]f]ae`beffadffafcf^[ac^dWd^abe`[d`_be_BBBBB
@ILLUMINA-FFC6C4_0005:7:1:2497:1094#0/1
GACGCTCACTCTCTCTGGTATAACTTCACCATCATTCATTTGCCCAGACATGGGCAACAGTGGTGTGAGGTCCA
+ILLUMINA-FFC6C4_0005:7:1:2497:1094#0/1
cbbd][dbdffffcbcccRa^ab^cff[d^Qaa^f[fefg_gcec`_f[Y^a^_ccaa_aZ`dYa[`Y``Y^Z[
@ILLUMINA-FFC6C4_0005:7:1:2730:1091#0/1
GGAACACACAGCTTCCCAGCTTTGGACAGTTGGTACAGCCTGAGGATGAGGGAAGCCAAGAACAAAAAACACCA
+ILLUMINA-FFC6C4_0005:7:1:2730:1091#0/1
ddaa`da`aacZa^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
I want to try MAQ (for the first time) for analysis of Illumina HiSeq human whole exome results, and I have two questions:
1. Is it ok to use hg19_chromFa.tar (from UCSC) as a reference, or should I run it again each chromosome individually ?
2. The text file I got from the HiSeq (which is fastq actually) is ok as an input for maq fasta2bfa command, or should I change its fastq format? I think that Hiseq output is already in the Sanger fastq format, but I'm not sure? below I copied the beginning of the txt file.
Thanks!
@ILLUMINA-FFC6C4_0005:7:1:1941:1087#0/1
CACATTGGATTGATCGGTCTCATTGGCCCCCCGGGAGAAGCTGGGGAGAAAGGAGATCAGGGGGTGCCAGGCGT
+ILLUMINA-FFC6C4_0005:7:1:1941:1087#0/1
faf\f_ccfffffSedaRe\dcdYffffcggg`g^ae`ca^RbaJ_VWW_Z\\Na`d``]a`bGM[UYVa`]`B
@ILLUMINA-FFC6C4_0005:7:1:2045:1092#0/1
GTGTGAATTTCATTTCCACATAAATTTTCTGAGCTGCATCACGGGAGATCCAGTTTGTACGAAGCCAGTTGTTT
+ILLUMINA-FFC6C4_0005:7:1:2045:1092#0/1
fffff_ffff[a\feaacafffffgfggcff]f]ae`beffadffafcf^[ac^dWd^abe`[d`_be_BBBBB
@ILLUMINA-FFC6C4_0005:7:1:2497:1094#0/1
GACGCTCACTCTCTCTGGTATAACTTCACCATCATTCATTTGCCCAGACATGGGCAACAGTGGTGTGAGGTCCA
+ILLUMINA-FFC6C4_0005:7:1:2497:1094#0/1
cbbd][dbdffffcbcccRa^ab^cff[d^Qaa^f[fefg_gcec`_f[Y^a^_ccaa_aZ`dYa[`Y``Y^Z[
@ILLUMINA-FFC6C4_0005:7:1:2730:1091#0/1
GGAACACACAGCTTCCCAGCTTTGGACAGTTGGTACAGCCTGAGGATGAGGGAAGCCAAGAACAAAAAACACCA
+ILLUMINA-FFC6C4_0005:7:1:2730:1091#0/1
ddaa`da`aacZa^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
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