I was able to get tophat running on colorspace reads by doing what many others have mentioned: Removing comment lines in .csfasta and .qual; and converting all -1 qualities to 0.
On 5/8 of my datasets, tophat works great. On the remaining 3 I get the following error.
Has anyone else seen an error like this? Is there a fix available?
On 5/8 of my datasets, tophat works great. On the remaining 3 I get the following error.
Code:
Traceback (most recent call last): File "/share/apps/tophat-1.1.0.Linux_x86_64/tophat", line 2174, in ? sys.exit(main()) File "/share/apps/tophat-1.1.0.Linux_x86_64/tophat", line 2133, in main user_supplied_juncs) File "/share/apps/tophat-1.1.0.Linux_x86_64/tophat", line 1848, in spliced_alignment segment_len) File "/share/apps/tophat-1.1.0.Linux_x86_64/tophat", line 1570, in split_reads split_record(read_name, read_seq, read_quals, output_files, offsets, color) File "/share/apps/tophat-1.1.0.Linux_x86_64/tophat", line 1503, in split_record read_seq_temp = convert_color_to_bp(read_seq) File "/share/apps/tophat-1.1.0.Linux_x86_64/tophat", line 1477, in convert_color_to_bp base = decode_dic[base+ch] KeyError: 'GN'
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