Hi,
I'm trying to figure out why I am getting such a low % of mapped reads (using tophat/bowtie). I'm still experimenting with parameters in bowtie, but thus far, I can't get much above 30%. I'm working with a new genome with plenty of gaps and things, so that might explain part of it. BUt I also don't fully understand the quality scores. Do these look funny to any of you? It seems to be the higher quality scores are on the end of these reads? (the Bs?). Any thoughts?
@HWI-EAS385_0044:2:1:4:1884#0/1
CAGCTGGNAGGCTCCACGGCGGGCGTGCGCCAAGTGCCGGGGCTGCACAACGGGAGCCAAGCCTTCCTCTTCTCA
+HWI-EAS385_0044:2:1:4:1884#0/1
\\X[\LTDTT_Vb__X_Z_V`XUceZcfcc_PTPKVb__\]bee]]X_BBBBBBBBBBBBBBBBBBBBBBBBBBB
@HWI-EAS385_0044:2:1:4:1477#0/1
GGGCCATNGCATCTGTGGGCACGGGAGGGGCCAGCACAGCCGCAGGACTACTGGCCGAGGCCCCCGCCGCGGCAG
+HWI-EAS385_0044:2:1:4:1477#0/1
ecdce[bE]`TTTSS\Wb\bTW^XNRMURVO\PX]Q`N^^R]SK\\\MVM\P\V^M[LPX`^BBBBBBBBBBBBB
@HWI-EAS385_0044:2:1:4:849#0/1
GTCGTACTCCTAGGGCTCGTGGTCGGCTGCGCCGGCTTGTCGTTTCGCTTCGCCTGCGGGCTGGGCTCCGTCGTG
+HWI-EAS385_0044:2:1:4:849#0/1
bXb_[`c_cc\U`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
I'm trying to figure out why I am getting such a low % of mapped reads (using tophat/bowtie). I'm still experimenting with parameters in bowtie, but thus far, I can't get much above 30%. I'm working with a new genome with plenty of gaps and things, so that might explain part of it. BUt I also don't fully understand the quality scores. Do these look funny to any of you? It seems to be the higher quality scores are on the end of these reads? (the Bs?). Any thoughts?
@HWI-EAS385_0044:2:1:4:1884#0/1
CAGCTGGNAGGCTCCACGGCGGGCGTGCGCCAAGTGCCGGGGCTGCACAACGGGAGCCAAGCCTTCCTCTTCTCA
+HWI-EAS385_0044:2:1:4:1884#0/1
\\X[\LTDTT_Vb__X_Z_V`XUceZcfcc_PTPKVb__\]bee]]X_BBBBBBBBBBBBBBBBBBBBBBBBBBB
@HWI-EAS385_0044:2:1:4:1477#0/1
GGGCCATNGCATCTGTGGGCACGGGAGGGGCCAGCACAGCCGCAGGACTACTGGCCGAGGCCCCCGCCGCGGCAG
+HWI-EAS385_0044:2:1:4:1477#0/1
ecdce[bE]`TTTSS\Wb\bTW^XNRMURVO\PX]Q`N^^R]SK\\\MVM\P\V^M[LPX`^BBBBBBBBBBBBB
@HWI-EAS385_0044:2:1:4:849#0/1
GTCGTACTCCTAGGGCTCGTGGTCGGCTGCGCCGGCTTGTCGTTTCGCTTCGCCTGCGGGCTGGGCTCCGTCGTG
+HWI-EAS385_0044:2:1:4:849#0/1
bXb_[`c_cc\U`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
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