Originally posted by adarob
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Originally posted by jamessmith01 View PostVersion 1.1.1 on the main page apparently includes fixes for these bugs...
Code:File "~/Tools/TopHat/tophat-1.1.4.Linux_x86_64/tophat", line 1520, in convert_color_to_bp base = decode_dic[base+ch] KeyError: 'CN'
Code:~/Tools/TopHat/tophat-1.1.4.Linux_x86_64/tophat -p 5 --library-type fr-secondstrand -CQ ~/References/bowtie-hg19/hg19-bowtie-cs sample_1_F3.csfasta samples_1_F3_QV.qual
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Hi,
Please can anyone who has used TopHat with SOLiD strand-specific data, say whether you used the fr-firststrand, fr-secondstarand or neither option?
To be clear, I'm using paired-end (50+25 bp), strand-specific SOLiD RNA-sequencing reads, and would like to know which option, if any, to use.
Thanks.
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